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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/3faa76e285caa806f097aa7080fbe397de9c5008">3faa76e2</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2020-05-29T11:31:41+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump d/changelog

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/22fe3e35f31f2f55a902e5138006b61c005a2a86">22fe3e35</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2020-05-29T11:32:46+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.17-200428</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/fc42abb3dfb33ccca769c6efc3bd453215e89b4f">fc42abb3</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2020-05-29T11:32:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.90_b6.17-200428'

Update to upstream version '1.90~b6.17-200428'

with Debian dir d1d41365240cb8d1ee4950ce2a2db64e812bcff5</pre>

</li>

</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">

plink.c

</a>

</li>

<li class="file-stats">

<a href="#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69">

plink_assoc.c

</a>

</li>

<li class="file-stats">

<a href="#a8e4f7e2f6aedfa2e57a4b081931760a1e0f1908">

plink_common.c

</a>

</li>

<li class="file-stats">

<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">

plink_data.c

</a>

</li>

<li class="file-stats">

<a href="#0759c782c4a630aa4d741961e3aec954ce174e93">

plink_filter.c

</a>

</li>

<li class="file-stats">

<a href="#9bb0322754d12ec877a1a8bf0beb2a76ab7656e4">

plink_glm.c

</a>

</li>

<li class="file-stats">

<a href="#a49f014090203c6a1777c23c77d3dc765795b040">

plink_homozyg.c

</a>

</li>

<li class="file-stats">

<a href="#61784fef9a51b22e54597c329feb8bb67829181b">

plink_lasso.c

</a>

</li>

<li class="file-stats">

<a href="#f040126837cea77b7b5f225f90d051a7d47d14be">

plink_ld.c

</a>

</li>

<li class="file-stats">

<a href="#ad63a8112365845088935bd1cf043fd5464ed840">

plink_misc.c

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink1.9 (1.90~b6.17-200428-1) UNRELEASED; urgency=medium</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream release.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org>  Fri, 29 May 2020 11:30:48 +0200</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">plink1.9 (1.90~b6.16-200219-1) unstable; urgency=medium</span>

</pre>

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2

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * New upstream release.</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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="93" 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">@@ -93,7 +93,7 @@</td>

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93

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<td class="diff-line-num new_line" data-linenumber="93" 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">

93

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" 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">

94

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<td class="diff-line-num new_line" data-linenumber="94" 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">

94

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" 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">

95

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" 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">

96

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90b6.1<span class="idiff left right">6</span>"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="96" 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">

96

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90b6.1<span class="idiff left right">7</span>"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" 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">

97

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<td class="diff-line-num new_line" data-linenumber="97" 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">

97

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" 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">

98

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90p"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" 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">

99

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<td class="diff-line-num new_line" data-linenumber="99" 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">

99

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="105" 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">@@ -105,7 +105,7 @@ static const char ver_str[] =</td>

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<td class="diff-line-num old_line" data-linenumber="105" 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">

105

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<td class="diff-line-num new_line" data-linenumber="105" 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">

105

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" 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">

106

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<td class="diff-line-num new_line" data-linenumber="106" 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">

106

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" 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">

107

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<td class="diff-line-num new_line" data-linenumber="107" 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">

107

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" 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">

108

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<td class="diff-line-num new_line old" data-linenumber="108" 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="LC108" class="line" lang="c">  <span class="s" style="color: #d14;">" (<span class="idiff left right">19 Feb</span> 2020)"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="109" 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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c">  <span class="s" style="color: #d14;">" (<span class="idiff left right">28 Apr</span> 2020)"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" 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">

110

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<td class="diff-line-num new_line" data-linenumber="110" 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">

110

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" 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">

111

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<td class="diff-line-num new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c">  <span class="s" style="color: #d14;">""</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2937" 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="2937" 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">@@ -2937,9 +2937,17 @@ int32_t init_delim_and_species(uint32_t flag_ct, char* flag_buf, uint32_t* flag_</td>

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<td class="diff-line-num old_line" data-linenumber="2937" 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">

2937

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<td class="diff-line-num new_line" data-linenumber="2937" 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">

2937

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<pre style="margin: 0;"> <span id="LC2937" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">init_delim_and_species_ret_INVALID_CMDLINE_WWA</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2938" 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">

2938

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<td class="diff-line-num new_line" data-linenumber="2938" 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">

2938

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<pre style="margin: 0;"> <span id="LC2938" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2939" 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">

2939

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<td class="diff-line-num new_line" data-linenumber="2939" 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">

2939

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<pre style="margin: 0;"> <span id="LC2939" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2940" 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">

2940

</td>

<td class="diff-line-num new_line old" data-linenumber="2940" 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="LC2940" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2941" 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">

2941

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<td class="diff-line-num new_line old" data-linenumber="2940" 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="LC2941" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2942" 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">

2942

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<td class="diff-line-num new_line old" data-linenumber="2940" 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="LC2942" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2940" 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">

2940

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<pre style="margin: 0;">+<span id="LC2940" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// bugfix (28 Apr 2020): We were segfaulting instead of printing an</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2941" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// appropriate error message when e.g. --autosome-num was specified yet</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="2942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2942" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// chrY was encountered.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2943" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// plink 2.0 fixed this issue by using -2 instead of -1 to indicate a null</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2944" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// xymt_code (-1 signals that there's nothing to worry about when</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2945" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr is specified).  It touches more code than I'd like,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2946" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// but I haven't gotten any related plink 2.0 bug reports for a long time,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2947" 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">

2947

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<pre style="margin: 0;">+<span id="LC2947" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// so we backport that fix.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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="2948" 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">

2948

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<pre style="margin: 0;">+<span id="LC2948" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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="2949" 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">

2949

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<pre style="margin: 0;">+<span id="LC2949" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2943" 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="2950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2950" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2943" 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">

2943

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<td class="diff-line-num new_line" data-linenumber="2951" 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">

2951

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<pre style="margin: 0;"> <span id="LC2951" class="line" lang="c">    <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2944" 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">

2944

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<td class="diff-line-num new_line" data-linenumber="2952" 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">

2952

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<pre style="margin: 0;"> <span id="LC2952" class="line" lang="c">    <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">autosome_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2953" 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">

2953

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<pre style="margin: 0;"> <span id="LC2953" class="line" lang="c">    <span class="n" style="color: #333;">set_bit</span><span class="p">(</span><span class="n" style="color: #333;">ii</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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2964" 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="2972" 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">@@ -2964,10 +2972,10 @@ int32_t init_delim_and_species(uint32_t flag_ct, char* flag_buf, uint32_t* flag_</td>

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<td class="diff-line-num new_line" data-linenumber="2972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2972" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2973" class="line" lang="c">      <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">autosome_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="2975" 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="LC2967" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2968" 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">

2968

</td>

<td class="diff-line-num new_line old" data-linenumber="2975" 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="LC2968" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2969" 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">

2969

</td>

<td class="diff-line-num new_line old" data-linenumber="2975" 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="LC2969" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2970" 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">

2970

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<td class="diff-line-num new_line old" data-linenumber="2975" 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="LC2970" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2971" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2975" 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">

2975

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<pre style="margin: 0;">+<span id="LC2975" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2971" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2976" 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">

2976

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<pre style="margin: 0;">+<span id="LC2976" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2971" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2977" 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">

2977

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<pre style="margin: 0;">+<span id="LC2977" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2971" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2978" 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">

2978

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<pre style="margin: 0;">+<span id="LC2978" class="line" lang="c">      <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2971" 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">

2971

</td>

<td class="diff-line-num new_line" data-linenumber="2979" 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">

2979

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<pre style="margin: 0;"> <span id="LC2979" class="line" lang="c">      <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2972" 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">

2972

</td>

<td class="diff-line-num new_line" data-linenumber="2980" 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">

2980

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<pre style="margin: 0;"> <span id="LC2980" class="line" lang="c">      <span class="n" style="color: #333;">fill_all_bits</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;">1</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;">haploid_mask</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2973" 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">

2973

</td>

<td class="diff-line-num new_line" data-linenumber="2981" 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">

2981

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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="c">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2980" 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="2988" 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">@@ -2980,27 +2988,27 @@ int32_t init_delim_and_species(uint32_t flag_ct, char* flag_buf, uint32_t* flag_</td>

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<td class="diff-line-num old_line" data-linenumber="2980" 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">

2980

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<td class="diff-line-num new_line" data-linenumber="2988" 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">

2988

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<pre style="margin: 0;"> <span id="LC2988" class="line" lang="c">      <span class="n" style="color: #333;">set_bit</span><span class="p">(</span><span class="n" style="color: #333;">ii</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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2981" 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">

2981

</td>

<td class="diff-line-num new_line" data-linenumber="2989" 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">

2989

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<pre style="margin: 0;"> <span id="LC2989" class="line" lang="c">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">param_idx</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;">param_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">param_ct</span><span class="p">;</span> <span class="n" style="color: #333;">param_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2982" 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">

2982

</td>

<td class="diff-line-num new_line" data-linenumber="2990" 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">

2990

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<pre style="margin: 0;"> <span id="LC2990" 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;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"no-x"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2983" 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">

2983

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<td class="diff-line-num new_line old" data-linenumber="2991" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2983" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2984" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2991" 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">

2991

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2991" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2984" 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">

2984

</td>

<td class="diff-line-num new_line" data-linenumber="2992" 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">

2992

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2992" class="line" lang="c">     <span class="n" style="color: #333;">clear_bit</span><span class="p">(</span><span class="n" style="color: #333;">ii</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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2985" 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">

2985

</td>

<td class="diff-line-num new_line" data-linenumber="2993" 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">

2993

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2993" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"no-y"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2986" 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">

2986

</td>

<td class="diff-line-num new_line old" data-linenumber="2994" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2986" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2987" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2994" 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">

2994

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2994" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2987" 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">

2987

</td>

<td class="diff-line-num new_line" data-linenumber="2995" 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">

2995

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2995" class="line" lang="c">     <span class="n" style="color: #333;">clear_bit</span><span class="p">(</span><span class="n" style="color: #333;">ii</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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2988" 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">

2988

</td>

<td class="diff-line-num new_line" data-linenumber="2996" 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">

2996

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2996" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"no-xy"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2989" 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">

2989

</td>

<td class="diff-line-num new_line old" data-linenumber="2997" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2989" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2990" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2997" 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">

2997

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2997" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2990" 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">

2990

</td>

<td class="diff-line-num new_line" data-linenumber="2998" 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">

2998

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2998" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"no-mt"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2991" 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">

2991

</td>

<td class="diff-line-num new_line old" data-linenumber="2999" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2991" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2992" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2999" 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">

2999

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2999" class="line" lang="c">     <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2992" 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">

2992

</td>

<td class="diff-line-num new_line" data-linenumber="3000" 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">

3000

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3000" class="line" lang="c">   <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2993" 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">

2993

</td>

<td class="diff-line-num new_line" data-linenumber="3001" 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">

3001

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3001" 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;">"Error: Invalid --chr-set parameter '%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;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2994" 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">

2994

</td>

<td class="diff-line-num new_line" data-linenumber="3002" 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">

3002

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3002" class="line" lang="c">     <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">init_delim_and_species_ret_INVALID_CMDLINE_WWA</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2995" 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">

2995

</td>

<td class="diff-line-num new_line" data-linenumber="3003" 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">

3003

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3003" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2996" 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">

2996

</td>

<td class="diff-line-num new_line" data-linenumber="3004" 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">

3004

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3004" class="line" lang="c">      <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2997" 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">

2997

</td>

<td class="diff-line-num new_line old" data-linenumber="3005" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2997" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2998" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3005" 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">

3005

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3005" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2998" 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">

2998

</td>

<td class="diff-line-num new_line" data-linenumber="3006" 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">

3006

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3006" class="line" lang="c">   <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2999" 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">

2999

</td>

<td class="diff-line-num new_line old" data-linenumber="3007" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2999" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3000" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3007" 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">

3007

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3007" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3000" 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">

3000

</td>

<td class="diff-line-num new_line" data-linenumber="3008" 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">

3008

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3008" class="line" lang="c">   <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3001" 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">

3001

</td>

<td class="diff-line-num new_line old" data-linenumber="3009" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3001" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3002" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3009" 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">

3009

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3009" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3002" 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">

3002

</td>

<td class="diff-line-num new_line" data-linenumber="3010" 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">

3010

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3010" class="line" lang="c">   <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3003" 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">

3003

</td>

<td class="diff-line-num new_line old" data-linenumber="3011" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3003" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3004" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3011" 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">

3011

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3011" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3004" 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">

3004

</td>

<td class="diff-line-num new_line" data-linenumber="3012" 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">

3012

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3012" class="line" lang="c">   <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3005" 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">

3005

</td>

<td class="diff-line-num new_line" data-linenumber="3013" 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">

3013

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3013" class="line" lang="c">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3006" 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">

3006

</td>

<td class="diff-line-num new_line" data-linenumber="3014" 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">

3014

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3014" class="line" lang="c">   <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4238" 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="4246" 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">@@ -4238,7 +4246,7 @@ int32_t main(int32_t argc, char** argv) {</td>

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<td class="diff-line-num old_line" data-linenumber="4238" 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">

4238

</td>

<td class="diff-line-num new_line" data-linenumber="4246" 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">

4246

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4246" class="line" lang="c">          <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --autosome-xy cannot be used with --autosome.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4239" 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">

4239

</td>

<td class="diff-line-num new_line" data-linenumber="4247" 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">

4247

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4247" class="line" lang="c">     <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4240" 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">

4240

</td>

<td class="diff-line-num new_line" data-linenumber="4248" 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">

4248

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4248" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4241" 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">

4241

</td>

<td class="diff-line-num new_line old" data-linenumber="4249" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4241" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4242" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4249" 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">

4249

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4249" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4242" 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">

4242

</td>

<td class="diff-line-num new_line" data-linenumber="4250" 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">

4250

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4250" class="line" lang="c">     <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --autosome-xy used with a species lacking an XY region.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4243" 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">

4243

</td>

<td class="diff-line-num new_line" data-linenumber="4251" 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">

4251

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4251" class="line" lang="c">     <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4244" 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">

4244

</td>

<td class="diff-line-num new_line" data-linenumber="4252" 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">

4252

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4252" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9269" 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="9277" 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">@@ -9269,7 +9277,7 @@ int32_t main(int32_t argc, char** argv) {</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9269" 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">

9269

</td>

<td class="diff-line-num new_line" data-linenumber="9277" 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">

9277

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9277" class="line" lang="c">        <span class="n" style="color: #333;">set_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">SET_COMPLEMENTS</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">SET_C_PREFIX</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">SET_MAKE_COLLAPSE_GROUP</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9270" 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">

9270

</td>

<td class="diff-line-num new_line" data-linenumber="9278" 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">

9278

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9278" class="line" lang="c">   <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_param_zero</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9271" 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">

9271

</td>

<td class="diff-line-num new_line" data-linenumber="9279" 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">

9279

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9279" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argptr2</span><span class="p">,</span> <span class="s" style="color: #d14;">"erge-x"</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9272" 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">

9272

</td>

<td class="diff-line-num new_line old" data-linenumber="9280" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9272" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xymt_codes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">XY_OFFSET</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="9273" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9280" 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">

9280

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9280" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xymt_codes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">XY_OFFSET</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9273" 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">

9273

</td>

<td class="diff-line-num new_line" data-linenumber="9281" 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">

9281

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9281" class="line" lang="c">     <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --merge-x must be used with a chromosome set containing X and XY codes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9274" 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">

9274

</td>

<td class="diff-line-num new_line" data-linenumber="9282" 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">

9282

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9282" class="line" lang="c">     <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="9275" 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">

9275

</td>

<td class="diff-line-num new_line" data-linenumber="9283" 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">

9283

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9283" class="line" lang="c">   <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10801" 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="10809" 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">@@ -10801,9 +10809,6 @@ int32_t main(int32_t argc, char** argv) {</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10801" 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">

10801

</td>

<td class="diff-line-num new_line" data-linenumber="10809" 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">

10809

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10809" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10802" 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">

10802

</td>

<td class="diff-line-num new_line" data-linenumber="10810" 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">

10810

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10810" 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;">argptr2</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10803" 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">

10803

</td>

<td class="diff-line-num new_line" data-linenumber="10811" 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">

10811

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10811" class="line" lang="c">          <span class="n" style="color: #333;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">LD_R2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10804" 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">

10804

</td>

<td class="diff-line-num new_line old" data-linenumber="10812" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10804" 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;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">window_r2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10805" 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">

10805

</td>

<td class="diff-line-num new_line old" data-linenumber="10812" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10805" class="line" lang="c">    <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --ld-window-r2 flag cannot be used with --r.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10806" 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">

10806

</td>

<td class="diff-line-num new_line old" data-linenumber="10812" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10806" class="line" lang="c">          <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10807" 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">

10807

</td>

<td class="diff-line-num new_line" data-linenumber="10812" 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">

10812

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10812" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10808" 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">

10808

</td>

<td class="diff-line-num new_line" data-linenumber="10813" 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">

10813

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10813" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matrix_flag_state</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10809" 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">

10809

</td>

<td class="diff-line-num new_line" data-linenumber="10814" 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">

10814

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10814" class="line" lang="c">    <span class="n" style="color: #333;">matrix_flag_state</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11402" 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="11407" 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">@@ -11402,7 +11407,7 @@ int32_t main(int32_t argc, char** argv) {</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11402" 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">

11402

</td>

<td class="diff-line-num new_line" data-linenumber="11407" 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">

11407

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11407" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MISC_MERGEX</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11403" 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">

11403

</td>

<td class="diff-line-num new_line" data-linenumber="11408" 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">

11408

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11408" class="line" lang="c">          <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --split-x cannot be used with --merge-x.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11404" 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">

11404

</td>

<td class="diff-line-num new_line" data-linenumber="11409" 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">

11409

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11409" class="line" lang="c">          <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11405" 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">

11405

</td>

<td class="diff-line-num new_line old" data-linenumber="11410" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11405" 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;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xymt_codes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">XY_OFFSET</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="11406" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11410" 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">

11410

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11410" 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;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xymt_codes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">XY_OFFSET</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11406" 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">

11406

</td>

<td class="diff-line-num new_line" data-linenumber="11411" 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">

11411

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11411" class="line" lang="c">    <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --split-x must be used with a chromosome set containing X and XY codes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11407" 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">

11407

</td>

<td class="diff-line-num new_line" data-linenumber="11412" 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">

11412

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11412" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11408" 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">

11408

</td>

<td class="diff-line-num new_line" data-linenumber="11413" 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">

11413

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11413" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69"><strong>plink_assoc.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6318" 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="6318" 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">@@ -6318,7 +6318,7 @@ int32_t model_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, cha</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6318" 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">

6318

</td>

<td class="diff-line-num new_line" data-linenumber="6318" 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">

6318

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6318" class="line" lang="c">    <span class="n" style="color: #333;">g_het_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">het_cts</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6319" 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">

6319

</td>

<td class="diff-line-num new_line" data-linenumber="6319" 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">

6319

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6319" class="line" lang="c">    <span class="n" style="color: #333;">g_homcom_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homcom_cts</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6320" 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">

6320

</td>

<td class="diff-line-num new_line" data-linenumber="6320" 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">

6320

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6320" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6321" 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">

6321

</td>

<td class="diff-line-num new_line old" data-linenumber="6321" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6321" class="line" lang="c">  <span class="n" style="color: #333;">gender_req</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">chrom_mask</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x_code</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">model_assoc</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(((</span></span><span class="n" style="color: #333;"><span class="idiff">y_code</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">))));</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6322" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6321" 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">

6321

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6321" class="line" lang="c">  <span class="n" style="color: #333;">gender_req</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom_info_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">chrom_mask</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x_code</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">model_assoc</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(((</span></span><span class="n" style="color: #333;"><span class="idiff">y_code</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></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;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">))));</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6322" 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">

6322

</td>

<td class="diff-line-num new_line" data-linenumber="6322" 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">

6322

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<pre style="margin: 0;"> <span id="LC6322" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gender_req</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6323" 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">

6323

</td>

<td class="diff-line-num new_line" data-linenumber="6323" 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">

6323

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<pre style="margin: 0;"> <span id="LC6323" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_ul</span><span class="p">(</span><span class="n" style="color: #333;">pheno_nm_ctv2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_sample_nonmale_include2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6324" 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">

6324

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<td class="diff-line-num new_line" data-linenumber="6324" 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">

6324

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<pre style="margin: 0;"> <span id="LC6324" class="line" lang="c">   <span class="n" style="color: #333;">bigstack_alloc_ul</span><span class="p">(</span><span class="n" style="color: #333;">pheno_nm_ctv2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8109" 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="8109" 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">@@ -8109,7 +8109,7 @@ int32_t qassoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* ou</td>

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<td class="diff-line-num old_line" data-linenumber="8109" 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">

8109

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<td class="diff-line-num new_line" data-linenumber="8109" 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">

8109

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<pre style="margin: 0;"> <span id="LC8109" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8110" 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">

8110

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<td class="diff-line-num new_line" data-linenumber="8110" 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">

8110

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<pre style="margin: 0;"> <span id="LC8110" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_thread_ct</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8111" 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">

8111

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<td class="diff-line-num new_line" data-linenumber="8111" 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">

8111

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<pre style="margin: 0;"> <span id="LC8111" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">perm_pass_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8112" 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">

8112

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<td class="diff-line-num new_line old" data-linenumber="8112" 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="LC8112" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mt_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8113" 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="8112" 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">

8112

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<pre style="margin: 0;">+<span id="LC8112" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mt_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8113" 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">

8113

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<td class="diff-line-num new_line" data-linenumber="8113" 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">

8113

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<pre style="margin: 0;"> <span id="LC8113" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hh_exists</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">mt_exists</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8114" 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">

8114

</td>

<td class="diff-line-num new_line" data-linenumber="8114" 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">

8114

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<pre style="margin: 0;"> <span id="LC8114" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8115" 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">

8115

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<td class="diff-line-num new_line" data-linenumber="8115" 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">

8115

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<pre style="margin: 0;"> <span id="LC8115" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x11</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9150" 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="9150" 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">@@ -9150,8 +9150,8 @@ int32_t gxe_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outn</td>

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<td class="diff-line-num old_line" data-linenumber="9150" 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">

9150

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<td class="diff-line-num new_line" data-linenumber="9150" 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">

9150

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<pre style="margin: 0;"> <span id="LC9150" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_sample_ctv2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9151" 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">

9151

</td>

<td class="diff-line-num new_line" data-linenumber="9151" 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">

9151

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<pre style="margin: 0;"> <span id="LC9151" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_group1_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9152" 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">

9152

</td>

<td class="diff-line-num new_line" data-linenumber="9152" 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">

9152

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<pre style="margin: 0;"> <span id="LC9152" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_group2_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9153" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]);</span></span>

</pre>

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9154

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<td class="diff-line-num new_line old" data-linenumber="9153" 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="LC9154" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mt_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9153" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9154" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mt_exists</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]);</span></span>

</pre>

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9155

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<td class="diff-line-num new_line" data-linenumber="9155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9155" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">skip_y</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="LC9156" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pheno_sum_g1</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 new_line" data-linenumber="9157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9157" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pheno_ssq_g1</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 old_line" data-linenumber="10054" 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="10054" 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">@@ -10054,7 +10054,7 @@ int32_t testmiss(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*</td>

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<pre style="margin: 0;"> <span id="LC10054" class="line" lang="c">  <span class="n" style="color: #333;">cur_ctrl_ct_recip</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="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)((</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span><span class="n" style="color: #333;">ctrl_ct</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC10055" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// Y chromosome requires special handling--only male genotypes should be</span></span>

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<td class="diff-line-num new_line" data-linenumber="10056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10056" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// considered.</span></span>

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<pre style="margin: 0;">-<span id="LC10057" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></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;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">)))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC10057" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></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;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">)))</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="10058" 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">

10058

</td>

<td class="diff-line-num new_line" data-linenumber="10058" 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">

10058

</td>

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<pre style="margin: 0;"> <span id="LC10058" class="line" lang="c">    <span class="n" style="color: #333;">skip_y</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10059" 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">

10059

</td>

<td class="diff-line-num new_line" data-linenumber="10059" 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">

10059

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<pre style="margin: 0;"> <span id="LC10059" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">case_ct_y</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;">ctrl_ct_y</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10060" 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">

10060

</td>

<td class="diff-line-num new_line" data-linenumber="10060" 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">

10060

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10060" class="line" lang="c">    <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: --test-missing is skipping Y chromosome since at least one male case</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">and one male control are necessary.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11121" 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="11121" 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">@@ -11121,7 +11121,7 @@ int32_t cmh_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*</td>

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<td class="diff-line-num old_line" data-linenumber="11121" 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">

11121

</td>

<td class="diff-line-num new_line" data-linenumber="11121" 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">

11121

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11121" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">putc_checked</span><span class="p">(</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="11122" 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">

11122

</td>

<td class="diff-line-num new_line" data-linenumber="11122" 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">

11122

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11122" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">cmh_assoc_ret_WRITE_FAIL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11123" 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">

11123

</td>

<td class="diff-line-num new_line" data-linenumber="11123" 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">

11123

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11123" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11124" 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">

11124

</td>

<td class="diff-line-num new_line old" data-linenumber="11124" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11124" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="11125" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11124" 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">

11124

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11124" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11125" 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">

11125

</td>

<td class="diff-line-num new_line" data-linenumber="11125" 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">

11125

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11125" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11126" 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">

11126

</td>

<td class="diff-line-num new_line" data-linenumber="11126" 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">

11126

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11126" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11127" 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">

11127

</td>

<td class="diff-line-num new_line" data-linenumber="11127" 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">

11127

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11127" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alloc_raw_haploid_filters</span><span class="p">(</span><span class="n" style="color: #333;">unfiltered_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">hh_or_mt_exists</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_include2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11464" 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="11464" 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">@@ -11464,7 +11464,7 @@ int32_t cmh2_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* out</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11464" 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">

11464

</td>

<td class="diff-line-num new_line" data-linenumber="11464" 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">

11464

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11464" 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;">mi_buf</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11465" 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">

11465

</td>

<td class="diff-line-num new_line" data-linenumber="11465" 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">

11465

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11465" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">cmh2_assoc_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11466" 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">

11466

</td>

<td class="diff-line-num new_line" data-linenumber="11466" 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">

11466

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11466" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11467" 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">

11467

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<td class="diff-line-num new_line old" data-linenumber="11467" 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="LC11467" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11468" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11467" 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">

11467

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11467" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11468" 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">

11468

</td>

<td class="diff-line-num new_line" data-linenumber="11468" 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">

11468

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<pre style="margin: 0;"> <span id="LC11468" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11469" 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">

11469

</td>

<td class="diff-line-num new_line" data-linenumber="11469" 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">

11469

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11469" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11470" 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">

11470

</td>

<td class="diff-line-num new_line" data-linenumber="11470" 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">

11470

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11470" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alloc_raw_haploid_filters</span><span class="p">(</span><span class="n" style="color: #333;">unfiltered_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">hh_or_mt_exists</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_include2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11726" 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="11726" 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">@@ -11726,7 +11726,7 @@ int32_t homog_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* ou</td>

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<td class="diff-line-num old_line" data-linenumber="11726" 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">

11726

</td>

<td class="diff-line-num new_line" data-linenumber="11726" 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">

11726

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11726" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// misaligned for backward compatibility</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11727" 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">

11727

</td>

<td class="diff-line-num new_line" data-linenumber="11727" 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">

11727

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11727" class="line" lang="c">  <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_textbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">" CHR %%%us   A1   A2      F_A      F_U      N_A      N_U     TEST      CHISQ   DF          P         OR</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;">plink_maxsnp</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11728" 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">

11728

</td>

<td class="diff-line-num new_line" data-linenumber="11728" 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">

11728

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11728" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">g_textbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"SNP"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11729" 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">

11729

</td>

<td class="diff-line-num new_line old" data-linenumber="11729" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11729" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="11730" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11729" 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">

11729

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11729" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11730" 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">

11730

</td>

<td class="diff-line-num new_line" data-linenumber="11730" 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">

11730

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11730" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11731" 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">

11731

</td>

<td class="diff-line-num new_line" data-linenumber="11731" 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">

11731

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11731" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="11732" 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">

11732

</td>

<td class="diff-line-num new_line" data-linenumber="11732" 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">

11732

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11732" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alloc_raw_haploid_filters</span><span class="p">(</span><span class="n" style="color: #333;">unfiltered_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">hh_or_mt_exists</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_include2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_hh_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a8e4f7e2f6aedfa2e57a4b081931760a1e0f1908">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#a8e4f7e2f6aedfa2e57a4b081931760a1e0f1908"><strong>plink_common.c</strong></a>

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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4397" 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">@@ -4397,12 +4397,12 @@ void init_species(uint32_t species_code, Chrom_info* chrom_info_ptr) {</td>

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4397

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4397

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<pre style="margin: 0;"> <span id="LC4397" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// sheep: 26, X, Y</span></span>

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<td class="diff-line-num old_line" data-linenumber="4398" 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">

4398

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4398

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<pre style="margin: 0;"> <span id="LC4398" class="line" lang="c">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">species_xymt_codes</span><span class="p">[]</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="4399" 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">

4399

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<td class="diff-line-num new_line" data-linenumber="4399" 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">

4399

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<pre style="margin: 0;"> <span id="LC4399" class="line" lang="c">    <span class="mi" style="color: #099;">23</span><span class="p">,</span> <span class="mi" style="color: #099;">24</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">,</span> <span class="mi" style="color: #099;">26</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4400" 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">

4400

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<td class="diff-line-num new_line old" data-linenumber="4400" 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="LC4400" class="line" lang="c">    <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4401" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4400" 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">

4400

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<pre style="margin: 0;">+<span id="LC4400" class="line" lang="c">    <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4401" 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">

4401

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<td class="diff-line-num new_line" data-linenumber="4401" 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">

4401

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<pre style="margin: 0;"> <span id="LC4401" class="line" lang="c">    <span class="mi" style="color: #099;">39</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">41</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4402" 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">

4402

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<td class="diff-line-num new_line old" data-linenumber="4402" 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="LC4402" class="line" lang="c">    <span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4403" 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">

4403

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<td class="diff-line-num new_line old" data-linenumber="4402" 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="LC4403" class="line" lang="c">    <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4404" 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">

4404

</td>

<td class="diff-line-num new_line old" data-linenumber="4402" 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="LC4404" class="line" lang="c">    <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4405" 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">

4405

</td>

<td class="diff-line-num new_line old" data-linenumber="4402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4405" class="line" lang="c">    <span class="mi" style="color: #099;">27</span><span class="p">,</span> <span class="mi" style="color: #099;">28</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4406" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4402" 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">

4402

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4402" class="line" lang="c">    <span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4406" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4403" 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">

4403

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4403" class="line" lang="c">    <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4406" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4404" 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">

4404

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4404" class="line" lang="c">    <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4406" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4405" 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">

4405

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4405" class="line" lang="c">    <span class="mi" style="color: #099;">27</span><span class="p">,</span> <span class="mi" style="color: #099;">28</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4406" 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">

4406

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<td class="diff-line-num new_line" data-linenumber="4406" 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">

4406

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<pre style="margin: 0;"> <span id="LC4406" 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;">species_autosome_ct</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">22</span><span class="p">,</span> <span class="mi" style="color: #099;">29</span><span class="p">,</span> <span class="mi" style="color: #099;">38</span><span class="p">,</span> <span class="mi" style="color: #099;">31</span><span class="p">,</span> <span class="mi" style="color: #099;">19</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">26</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4407" 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">

4407

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<td class="diff-line-num new_line" data-linenumber="4407" 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">

4407

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<pre style="margin: 0;"> <span id="LC4407" 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;">species_max_code</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">26</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">28</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4408" 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">

4408

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<td class="diff-line-num new_line" data-linenumber="4408" 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">

4408

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<pre style="margin: 0;"> <span id="LC4408" class="line" lang="c">  <span class="n" style="color: #333;">fill_ulong_zero</span><span class="p">(</span><span class="n" style="color: #333;">CHROM_MASK_WORDS</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;">chrom_mask</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4463" 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="4463" 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">@@ -4463,7 +4463,7 @@ void init_default_chrom_mask(Chrom_info* chrom_info_ptr) {</td>

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<td class="diff-line-num old_line" data-linenumber="4463" 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">

4463

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<td class="diff-line-num new_line" data-linenumber="4463" 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">

4463

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<pre style="margin: 0;"> <span id="LC4463" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// --chr-set support</span></span>

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<td class="diff-line-num old_line" data-linenumber="4464" 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">

4464

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<td class="diff-line-num new_line" data-linenumber="4464" 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">

4464

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<pre style="margin: 0;"> <span id="LC4464" 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;">uint32_t</span> <span class="n" style="color: #333;">xymt_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;">xymt_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">XYMT_OFFSET_CT</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">xymt_idx</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4465" 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">

4465

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<td class="diff-line-num new_line" data-linenumber="4465" 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">

4465

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<pre style="margin: 0;"> <span id="LC4465" class="line" lang="c">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cur_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">xymt_idx</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4466" 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">

4466

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<td class="diff-line-num new_line old" data-linenumber="4466" 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="LC4466" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4467" 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="4466" 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">

4466

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<pre style="margin: 0;">+<span id="LC4466" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4467" 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">

4467

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<td class="diff-line-num new_line" data-linenumber="4467" 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">

4467

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<pre style="margin: 0;"> <span id="LC4467" class="line" lang="c">   <span class="n" style="color: #333;">set_bit</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">xymt_idx</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;">chrom_mask</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4468" 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">

4468

</td>

<td class="diff-line-num new_line" data-linenumber="4468" 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">

4468

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<pre style="margin: 0;"> <span id="LC4468" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4469" 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">

4469

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<td class="diff-line-num new_line" data-linenumber="4469" 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">

4469

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<pre style="margin: 0;"> <span id="LC4469" 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="8263" 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="8263" 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">@@ -8263,13 +8263,13 @@ uint32_t count_non_autosomal_markers(const Chrom_info* chrom_info_ptr, const uin</td>

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<td class="diff-line-num old_line" data-linenumber="8263" 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">

8263

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<td class="diff-line-num new_line" data-linenumber="8263" 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">

8263

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<pre style="margin: 0;"> <span id="LC8263" class="line" lang="c">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">y_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8264" 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">

8264

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<td class="diff-line-num new_line" data-linenumber="8264" 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">

8264

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<pre style="margin: 0;"> <span id="LC8264" class="line" lang="c">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mt_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8265" 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">

8265

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<td class="diff-line-num new_line" data-linenumber="8265" 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">

8265

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<pre style="margin: 0;"> <span id="LC8265" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8266" 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">

8266

</td>

<td class="diff-line-num new_line old" data-linenumber="8266" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8266" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8267" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8266" 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">

8266

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8266" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8267" 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">

8267

</td>

<td class="diff-line-num new_line" data-linenumber="8267" 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">

8267

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8267" class="line" lang="c">    <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">x_code</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8268" 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">

8268

</td>

<td class="diff-line-num new_line" data-linenumber="8268" 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">

8268

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8268" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8269" 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">

8269

</td>

<td class="diff-line-num new_line old" data-linenumber="8269" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8269" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8270" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8269" 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">

8269

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8269" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8270" 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">

8270

</td>

<td class="diff-line-num new_line" data-linenumber="8270" 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">

8270

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8270" class="line" lang="c">    <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8271" 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">

8271

</td>

<td class="diff-line-num new_line" data-linenumber="8271" 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">

8271

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8271" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8272" 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">

8272

</td>

<td class="diff-line-num new_line old" data-linenumber="8272" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8272" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_mt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">mt_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8273" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8272" 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">

8272

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8272" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_mt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">mt_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8273" 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">

8273

</td>

<td class="diff-line-num new_line" data-linenumber="8273" 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">

8273

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8273" class="line" lang="c">    <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">mt_code</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8274" 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">

8274

</td>

<td class="diff-line-num new_line" data-linenumber="8274" 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">

8274

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8274" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8275" 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">

8275

</td>

<td class="diff-line-num new_line" data-linenumber="8275" 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">

8275

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8275" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ct</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8286" 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="8286" 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">@@ -8286,13 +8286,13 @@ int32_t conditional_allocate_non_autosomal_markers(const Chrom_info* chrom_info_</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8286" 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">

8286

</td>

<td class="diff-line-num new_line" data-linenumber="8286" 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">

8286

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8286" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_set</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;">haploid_mask</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8287" 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">

8287

</td>

<td class="diff-line-num new_line" data-linenumber="8287" 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">

8287

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8287" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newly_excluded_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_ct</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8288" 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">

8288

</td>

<td class="diff-line-num new_line" data-linenumber="8288" 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">

8288

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8288" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8289" 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">

8289

</td>

<td class="diff-line-num new_line old" data-linenumber="8289" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8289" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8290" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8289" 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">

8289

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8289" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_x</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8290" 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">

8290

</td>

<td class="diff-line-num new_line" data-linenumber="8290" 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">

8290

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8290" class="line" lang="c">      <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude_orig</span><span class="p">,</span> <span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8291" 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">

8291

</td>

<td class="diff-line-num new_line" data-linenumber="8291" 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">

8291

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8291" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8292" 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">

8292

</td>

<td class="diff-line-num new_line old" data-linenumber="8292" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8292" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8293" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8292" 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">

8292

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8292" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8293" 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">

8293

</td>

<td class="diff-line-num new_line" data-linenumber="8293" 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">

8293

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8293" class="line" lang="c">      <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude_orig</span><span class="p">,</span> <span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8294" 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">

8294

</td>

<td class="diff-line-num new_line" data-linenumber="8294" 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">

8294

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8294" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8295" 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">

8295

</td>

<td class="diff-line-num new_line old" data-linenumber="8295" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8295" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_mt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8296" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8295" 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">

8295

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8295" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count_mt</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8296" 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">

8296

</td>

<td class="diff-line-num new_line" data-linenumber="8296" 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">

8296

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8296" class="line" lang="c">      <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude_orig</span><span class="p">,</span> <span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8297" 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">

8297

</td>

<td class="diff-line-num new_line" data-linenumber="8297" 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">

8297

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8297" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8298" 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">

8298

</td>

<td class="diff-line-num new_line" data-linenumber="8298" 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">

8298

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8298" class="line" lang="c">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">newly_excluded_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">xymt_cts</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">];</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f101da6685d6d3284ff66b606e058f55eebde6b7">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13193" 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="13193" 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">@@ -13193,7 +13193,7 @@ int32_t recode(uint32_t recode_modifier, FILE* bedfile, uintptr_t bed_offset, ch</td>

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<pre style="margin: 0;"> <span id="LC13193" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// for backward compatibility, also exclude XY.  don't exclude custom name</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13194" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// chromosomes, though, since chromosome 0 was actually processed</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13195" 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">

13195

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<td class="diff-line-num new_line" data-linenumber="13195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13195" class="line" lang="c">    <span class="n" style="color: #333;">autosomal_marker_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">count_non_autosomal_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</span><span class="p">,</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13196" 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">

13196

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<td class="diff-line-num new_line old" data-linenumber="13196" 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="LC13196" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13197" 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="13196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13196" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13197" 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">

13197

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<pre style="margin: 0;"> <span id="LC13197" class="line" lang="c">      <span class="n" style="color: #333;">autosomal_marker_ct</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">count_chrom_markers</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">XY_OFFSET</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13198" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="13199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13199" 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;">autosomal_marker_ct</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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</table>

<br>

</li>

<li id="0759c782c4a630aa4d741961e3aec954ce174e93">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#0759c782c4a630aa4d741961e3aec954ce174e93"><strong>plink_filter.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1178" 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="1178" 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">@@ -1178,7 +1178,7 @@ int32_t load_oblig_missing(FILE* bedfile, uintptr_t bed_offset, uintptr_t unfilt</td>

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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">y_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">y_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1181" 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="LC1181" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1182" 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="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">));</span></span>

</pre>

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1182

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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="c">  <span class="n" style="color: #333;">Ll_str</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ll_ptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1184" 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">

1184

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<td class="diff-line-num new_line" data-linenumber="1184" 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">

1184

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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loadbuf</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1606" 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="1606" 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">@@ -1606,7 +1606,7 @@ int32_t mind_filter(FILE* bedfile, uintptr_t bed_offset, char* outname, char* ou</td>

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<td class="diff-line-num old_line" data-linenumber="1606" 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">

1606

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<td class="diff-line-num new_line" data-linenumber="1606" 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">

1606

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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1607" 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">

1607

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<td class="diff-line-num new_line" data-linenumber="1607" 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">

1607

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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">removed_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1608" 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">

1608

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<td class="diff-line-num new_line" data-linenumber="1608" 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">

1608

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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">y_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1609" 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">

1609

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<td class="diff-line-num new_line old" data-linenumber="1609" 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="LC1609" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1610" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1609" 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">

1609

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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1610" 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">

1610

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<td class="diff-line-num new_line" data-linenumber="1610" 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">

1610

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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nony_marker_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_ct</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1611" 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">

1611

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<td class="diff-line-num new_line" data-linenumber="1611" 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">

1611

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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1612" 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">

1612

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<td class="diff-line-num new_line" data-linenumber="1612" 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">

1612

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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mind_int_thresh</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2091" 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="2091" 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">@@ -2091,9 +2091,9 @@ int32_t calc_freqs_and_hwe(FILE* bedfile, char* outname, char* outname_end, uint</td>

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<td class="diff-line-num old_line" data-linenumber="2091" 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">

2091

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<td class="diff-line-num new_line" data-linenumber="2091" 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">

2091

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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="c">  <span class="n" style="color: #333;">loadbuf</span><span class="p">[</span><span class="n" style="color: #333;">unfiltered_sample_ctv2</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;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2092" 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">

2092

</td>

<td class="diff-line-num new_line" data-linenumber="2092" 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">

2092

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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="c">  <span class="n" style="color: #333;">init_quaterarr_from_inverted_bitarr</span><span class="p">(</span><span class="n" style="color: #333;">sample_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">unfiltered_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2093" 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">

2093

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<td class="diff-line-num new_line" data-linenumber="2093" 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">

2093

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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="c">  <span class="n" style="color: #333;">ii</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2094" 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">

2094

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<td class="diff-line-num new_line old" data-linenumber="2094" 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="LC2094" class="line" lang="c">  <span class="n" style="color: #333;">nonmales_needed</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;">is_split_chrom</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">ii</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2095" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2094" 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">

2094

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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="c">  <span class="n" style="color: #333;">nonmales_needed</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;">is_split_chrom</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">ii</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2095" 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">

2095

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<td class="diff-line-num new_line" data-linenumber="2095" 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">

2095

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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="c">  <span class="n" style="color: #333;">ii</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2096" 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">

2096

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<td class="diff-line-num new_line old" data-linenumber="2096" 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="LC2096" class="line" lang="c">  <span class="n" style="color: #333;">males_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonmales_needed</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;">is_split_chrom</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">ii</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2097" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2096" 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">

2096

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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="c">  <span class="n" style="color: #333;">males_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonmales_needed</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;">is_split_chrom</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">ii</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2097" 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">

2097

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<td class="diff-line-num new_line" data-linenumber="2097" 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">

2097

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<pre style="margin: 0;"> <span id="LC2097" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_ul</span><span class="p">(</span><span class="n" style="color: #333;">unfiltered_sample_ctv2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2098" 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">

2098

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<td class="diff-line-num new_line" data-linenumber="2098" 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">

2098

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<pre style="margin: 0;"> <span id="LC2098" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">calc_freqs_and_hwe_ret_NOMEM</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2099" 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">

2099

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<td class="diff-line-num new_line" data-linenumber="2099" 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">

2099

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<pre style="margin: 0;"> <span id="LC2099" 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="2507" 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="2507" 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">@@ -2507,7 +2507,7 @@ int32_t write_missingness_reports(FILE* bedfile, uintptr_t bed_offset, char* out</td>

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<td class="diff-line-num old_line" data-linenumber="2507" 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">

2507

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<td class="diff-line-num new_line" data-linenumber="2507" 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">

2507

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<pre style="margin: 0;"> <span id="LC2507" class="line" lang="c">  <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;">om_cluster_ref_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2508" 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">

2508

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<td class="diff-line-num new_line" data-linenumber="2508" 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">

2508

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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_om_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2509" 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">

2509

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<td class="diff-line-num new_line" data-linenumber="2509" 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">

2509

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<pre style="margin: 0;"> <span id="LC2509" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">y_code</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2510" 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">

2510

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<td class="diff-line-num new_line old" data-linenumber="2510" 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="LC2510" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2511" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2510" 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">

2510

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2510" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">y_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2511" 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">

2511

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<td class="diff-line-num new_line" data-linenumber="2511" 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">

2511

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2511" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2512" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_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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<pre style="margin: 0;"> <span id="LC2513" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">oblig_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="9bb0322754d12ec877a1a8bf0beb2a76ab7656e4">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#9bb0322754d12ec877a1a8bf0beb2a76ab7656e4"><strong>plink_glm.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3576" 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="3576" 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">@@ -3576,7 +3576,7 @@ int32_t glm_common_init(FILE* bedfile, uintptr_t bed_offset, uint32_t glm_modifi</td>

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<pre style="margin: 0;"> <span id="LC3576" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen_add</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="LC3577" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sex_covar_everywhere</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glm_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GLM_SEX</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3578" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">x_sex_interaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">glm_xchr_model</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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<pre style="margin: 0;">-<span id="LC3579" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">x_present</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3579" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">x_present</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3580" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hide_covar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glm_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GLM_HIDE_COVAR</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3581" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variation_in_sex</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;">// zero if no-x-sex specified</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3582" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">retval</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 old_line" data-linenumber="4501" 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="4501" 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">@@ -4501,7 +4501,7 @@ int32_t glm_linear_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset</td>

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<pre style="margin: 0;"> <span id="LC4501" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ujj</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4502" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ukk</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4503" class="line" lang="c">  <span class="n" style="color: #333;">numbuf</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="sc" style="color: #d14;">' '</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4504" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4505" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4504" 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">

4504

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<pre style="margin: 0;">+<span id="LC4504" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4505" 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">

4505

</td>

<td class="diff-line-num new_line" data-linenumber="4505" 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">

4505

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<pre style="margin: 0;"> <span id="LC4505" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4506" 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">

4506

</td>

<td class="diff-line-num new_line" data-linenumber="4506" 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">

4506

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<pre style="margin: 0;"> <span id="LC4506" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4507" 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">

4507

</td>

<td class="diff-line-num new_line" data-linenumber="4507" 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">

4507

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<pre style="margin: 0;"> <span id="LC4507" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_set_test</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6028" 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="6028" 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">@@ -6028,7 +6028,7 @@ int32_t glm_logistic_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offs</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6028" 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">

6028

</td>

<td class="diff-line-num new_line" data-linenumber="6028" 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">

6028

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<pre style="margin: 0;"> <span id="LC6028" class="line" lang="c">    <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Skipping --logistic since less than two phenotypes are present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6029" 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">

6029

</td>

<td class="diff-line-num new_line" data-linenumber="6029" 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">

6029

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6029" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">glm_logistic_assoc_ret_1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6030" 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">

6030

</td>

<td class="diff-line-num new_line" data-linenumber="6030" 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">

6030

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6030" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6031" 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">

6031

</td>

<td class="diff-line-num new_line old" data-linenumber="6031" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6031" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="6032" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6031" 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">

6031

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6031" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6032" 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">

6032

</td>

<td class="diff-line-num new_line" data-linenumber="6032" 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">

6032

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6032" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6033" 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">

6033

</td>

<td class="diff-line-num new_line" data-linenumber="6033" 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">

6033

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6033" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="6034" 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">

6034

</td>

<td class="diff-line-num new_line" data-linenumber="6034" 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">

6034

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6034" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_set_test</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7153" 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="7153" 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">@@ -7153,7 +7153,7 @@ int32_t glm_linear_nosnp(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7153" 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">

7153

</td>

<td class="diff-line-num new_line" data-linenumber="7153" 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">

7153

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7153" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">glm_linear_nosnp_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7154" 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">

7154

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<td class="diff-line-num new_line" data-linenumber="7154" 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">

7154

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7154" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7155" 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">

7155

</td>

<td class="diff-line-num new_line" data-linenumber="7155" 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">

7155

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7155" class="line" lang="c">  <span class="n" style="color: #333;">sample_valid_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">popcount_longs</span><span class="p">(</span><span class="n" style="color: #333;">load_mask</span><span class="p">,</span> <span class="n" style="color: #333;">unfiltered_sample_ctl</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="7156" 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">

7156

</td>

<td class="diff-line-num new_line old" data-linenumber="7156" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7156" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="7157" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7156" 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">

7156

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7156" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7157" 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">

7157

</td>

<td class="diff-line-num new_line" data-linenumber="7157" 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">

7157

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7157" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7158" 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">

7158

</td>

<td class="diff-line-num new_line" data-linenumber="7158" 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">

7158

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7158" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="7159" 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">

7159

</td>

<td class="diff-line-num new_line" data-linenumber="7159" 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">

7159

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7159" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">condition_mname</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">condition_fname</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8014" 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="8014" 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">@@ -8014,7 +8014,7 @@ int32_t glm_logistic_nosnp(pthread_t* threads, FILE* bedfile, uintptr_t bed_offs</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8014" 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">

8014

</td>

<td class="diff-line-num new_line" data-linenumber="8014" 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">

8014

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8014" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">glm_logistic_nosnp_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8015" 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">

8015

</td>

<td class="diff-line-num new_line" data-linenumber="8015" 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">

8015

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8015" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8016" 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">

8016

</td>

<td class="diff-line-num new_line" data-linenumber="8016" 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">

8016

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8016" class="line" lang="c">  <span class="n" style="color: #333;">sample_valid_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">popcount_longs</span><span class="p">(</span><span class="n" style="color: #333;">load_mask</span><span class="p">,</span> <span class="n" style="color: #333;">unfiltered_sample_ctl</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8017" 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">

8017

</td>

<td class="diff-line-num new_line old" data-linenumber="8017" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8017" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="8018" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8017" 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">

8017

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8017" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8018" 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">

8018

</td>

<td class="diff-line-num new_line" data-linenumber="8018" 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">

8018

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8018" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8019" 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">

8019

</td>

<td class="diff-line-num new_line" data-linenumber="8019" 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">

8019

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8019" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8020" 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">

8020

</td>

<td class="diff-line-num new_line" data-linenumber="8020" 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">

8020

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8020" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">condition_mname</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">condition_fname</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="a49f014090203c6a1777c23c77d3dc765795b040">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#a49f014090203c6a1777c23c77d3dc765795b040"><strong>plink_homozyg.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2543" 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="2543" 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">@@ -2543,7 +2543,7 @@ int32_t calc_homozyg(Homozyg_info* hp, FILE* bedfile, uintptr_t bed_offset, uint</td>

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<td class="diff-line-num old_line" data-linenumber="2543" 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">

2543

</td>

<td class="diff-line-num new_line" data-linenumber="2543" 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">

2543

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<pre style="margin: 0;"> <span id="LC2543" class="line" lang="c">      <span class="n" style="color: #333;">bigstack_end_alloc_ui</span><span class="p">(</span><span class="n" style="color: #333;">window_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">uidx_buf</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2544" 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">

2544

</td>

<td class="diff-line-num new_line" data-linenumber="2544" 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">

2544

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<pre style="margin: 0;"> <span id="LC2544" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">calc_homozyg_ret_NOMEM</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2545" 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">

2545

</td>

<td class="diff-line-num new_line" data-linenumber="2545" 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">

2545

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<pre style="margin: 0;"> <span id="LC2545" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2546" 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">

2546

</td>

<td class="diff-line-num new_line old" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2546" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2547" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2546" 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">

2546

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2546" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2547" 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">

2547

</td>

<td class="diff-line-num new_line" data-linenumber="2547" 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">

2547

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2547" 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_ul</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_male</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2548" 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">

2548

</td>

<td class="diff-line-num new_line" data-linenumber="2548" 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">

2548

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2548" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">calc_homozyg_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2549" 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">

2549

</td>

<td class="diff-line-num new_line" data-linenumber="2549" 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">

2549

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2549" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2567" 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="2567" 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">@@ -2567,7 +2567,7 @@ int32_t calc_homozyg(Homozyg_info* hp, FILE* bedfile, uintptr_t bed_offset, uint</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2567" 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">

2567

</td>

<td class="diff-line-num new_line" data-linenumber="2567" 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">

2567

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2567" 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;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_file_order</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2568" 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">

2568

</td>

<td class="diff-line-num new_line" data-linenumber="2568" 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">

2568

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2568" class="line" lang="c">    <span class="n" style="color: #333;">roh_list_chrom_starts</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">roh_ct</span><span class="p">;</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2569" 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">

2569

</td>

<td class="diff-line-num new_line" data-linenumber="2569" 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">

2569

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2569" class="line" lang="c">    <span class="n" style="color: #333;">chrom_end</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;">chrom_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2570" 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">

2570

</td>

<td class="diff-line-num new_line old" data-linenumber="2570" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2570" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">uii</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;">x_code</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2571" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2570" 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">

2570

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2570" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">uii</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;">x_code</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2571" 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">

2571

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<td class="diff-line-num new_line" data-linenumber="2571" 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">

2571

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<pre style="margin: 0;"> <span id="LC2571" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">haploid_mask</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="p">(</span><span class="n" style="color: #333;">uii</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;">mt_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2572" 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">

2572

</td>

<td class="diff-line-num new_line" data-linenumber="2572" 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">

2572

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<pre style="margin: 0;"> <span id="LC2572" class="line" lang="c">   <span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_end</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2573" 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">

2573

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<td class="diff-line-num new_line" data-linenumber="2573" 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">

2573

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<pre style="margin: 0;"> <span id="LC2573" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">bedfile</span><span class="p">,</span> <span class="n" style="color: #333;">bed_offset</span> <span class="o" style="font-weight: 600;">+</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;">marker_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">unfiltered_sample_ct4</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="61784fef9a51b22e54597c329feb8bb67829181b">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#61784fef9a51b22e54597c329feb8bb67829181b"><strong>plink_lasso.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="482" 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="482" 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">@@ -482,7 +482,7 @@ int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t* marker_re</td>

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<td class="diff-line-num old_line" data-linenumber="482" 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">

482

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<td class="diff-line-num new_line" data-linenumber="482" 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">

482

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">lasso_lambda_ret_NOMEM</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="483" 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">

483

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<td class="diff-line-num new_line" data-linenumber="483" 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">

483

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="484" 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">

484

</td>

<td class="diff-line-num new_line" data-linenumber="484" 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">

484

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c">    <span class="n" style="color: #333;">fill_quatervec_55</span><span class="p">(</span><span class="n" style="color: #333;">sample_valid_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="485" 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">

485

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<td class="diff-line-num new_line old" data-linenumber="485" 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="LC485" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="486" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="485" 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">

485

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="486" 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">

486

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<td class="diff-line-num new_line" data-linenumber="486" 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">

486

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c">      <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="487" 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">

487

</td>

<td class="diff-line-num new_line" data-linenumber="487" 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">

487

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="488" 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">

488

</td>

<td class="diff-line-num new_line" data-linenumber="488" 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">

488

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC488" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_male_include2</span><span class="p">;</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1135" 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="1135" 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">@@ -1135,7 +1135,7 @@ int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* out</td>

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<td class="diff-line-num old_line" data-linenumber="1135" 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">

1135

</td>

<td class="diff-line-num new_line" data-linenumber="1135" 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">

1135

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1135" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1136" 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">

1136

</td>

<td class="diff-line-num new_line" data-linenumber="1136" 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">

1136

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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="c">  <span class="n" style="color: #333;">fill_quatervec_55</span><span class="p">(</span><span class="n" style="color: #333;">sample_valid_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include2</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1137" 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">

1137

</td>

<td class="diff-line-num new_line" data-linenumber="1137" 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">

1137

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1137" class="line" lang="c">  <span class="n" style="color: #333;">fill_ulong_zero</span><span class="p">(</span><span class="n" style="color: #333;">unfiltered_marker_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">polymorphic_markers</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1138" 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">

1138

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<td class="diff-line-num new_line old" data-linenumber="1138" 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="LC1138" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1139" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1138" 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">

1138

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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1139" 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">

1139

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<td class="diff-line-num new_line" data-linenumber="1139" 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">

1139

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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="c">    <span class="n" style="color: #333;">hh_or_mt_exists</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">NXMHH_EXISTS</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1140" 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">

1140

</td>

<td class="diff-line-num new_line" data-linenumber="1140" 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">

1140

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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1141" 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">

1141

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<td class="diff-line-num new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alloc_collapsed_haploid_filters</span><span class="p">(</span><span class="n" style="color: #333;">pheno_nm2</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="n" style="color: #333;">unfiltered_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_valid_ct</span><span class="p">,</span> <span class="n" style="color: #333;">hh_or_mt_exists</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;">sample_include2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_male_include2</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="f040126837cea77b7b5f225f90d051a7d47d14be">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#f040126837cea77b7b5f225f90d051a7d47d14be"><strong>plink_ld.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2711" 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="2711" 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">@@ -2711,7 +2711,7 @@ uint32_t ld_regular_emitn(uint32_t overflow_ct, unsigned char* readbuf) {</td>

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<td class="diff-line-num old_line" data-linenumber="2711" 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">

2711

</td>

<td class="diff-line-num new_line" data-linenumber="2711" 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">

2711

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<pre style="margin: 0;"> <span id="LC2711" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">block_idx2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">block_end2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2712" 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">

2712

</td>

<td class="diff-line-num new_line" data-linenumber="2712" 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">

2712

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<pre style="margin: 0;"> <span id="LC2712" class="line" lang="c">      <span class="n" style="color: #333;">next_unset_ul_unsafe_ck</span><span class="p">(</span><span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">marker_uidx2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2713" 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">

2713

</td>

<td class="diff-line-num new_line" data-linenumber="2713" 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">

2713

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<pre style="margin: 0;"> <span id="LC2713" class="line" lang="c">      <span class="n" style="color: #333;">dxx</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dptr</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="2714" 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">

2714

</td>

<td class="diff-line-num new_line old" data-linenumber="2714" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2714" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">is_r2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fabs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">dxx</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">window_r2</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2715" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2714" 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">

2714

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2714" 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">fabs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">dxx</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">window_r2</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2715" 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">

2715

</td>

<td class="diff-line-num new_line" data-linenumber="2715" 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">

2715

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<pre style="margin: 0;"> <span id="LC2715" class="line" lang="c">   <span class="n" style="color: #333;">sptr_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">sptr_cur</span><span class="p">,</span> <span class="n" style="color: #333;">g_textbuf</span><span class="p">,</span> <span class="n" style="color: #333;">prefix_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2716" 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">

2716

</td>

<td class="diff-line-num new_line" data-linenumber="2716" 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">

2716

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<pre style="margin: 0;"> <span id="LC2716" class="line" lang="c">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_inter_chr</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2717" 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">

2717

</td>

<td class="diff-line-num new_line" data-linenumber="2717" 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">

2717

</td>

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<pre style="margin: 0;"> <span id="LC2717" class="line" lang="c">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_uidx2</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">chrom_end2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5312" 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="5312" 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">@@ -5312,7 +5312,7 @@ int32_t ld_report_dprime(pthread_t* threads, Ld_info* ldip, FILE* bedfile, uintp</td>

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<td class="diff-line-num old_line" data-linenumber="5312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5312" class="line" lang="c">  <span class="n" style="color: #333;">loadbuf</span><span class="p">[</span><span class="n" style="color: #333;">founder_ctl</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="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5313" class="line" lang="c">  <span class="n" style="color: #333;">fill_all_bits</span><span class="p">(</span><span class="n" style="color: #333;">founder_ct</span><span class="p">,</span> <span class="n" style="color: #333;">dummy_nm</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5314" 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">

5314

</td>

<td class="diff-line-num new_line" data-linenumber="5314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5314" class="line" lang="c">  <span class="n" style="color: #333;">g_ld_thread_wkspace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nullptr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="5315" 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="LC5315" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5316" 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="5315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5315" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5316" 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;">get_chrom_start_vidx</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</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;">x_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5317" 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">

5317

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<td class="diff-line-num new_line" data-linenumber="5317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5317" class="line" lang="c">    <span class="n" style="color: #333;">chrom_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_chrom_end_vidx</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</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;">x_code</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5318" class="line" lang="c">    <span class="n" style="color: #333;">chrom_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">popcount_bit_idx</span><span class="p">(</span><span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">uii</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5863" 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="5863" 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">@@ -5863,6 +5863,8 @@ int32_t ld_report_regular(pthread_t* threads, Ld_info* ldip, FILE* bedfile, uint</td>

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<td class="diff-line-num old_line" data-linenumber="5863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5863" class="line" lang="c">  <span class="n" style="color: #333;">g_ld_is_first_block</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;">parallel_idx</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5864" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_ld_is_r2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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</td>

<td class="diff-line-num new_line" data-linenumber="5865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5865" class="line" lang="c">    <span class="n" style="color: #333;">g_ld_window_r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ldip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">window_r2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5866" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5866" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5866" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5867" class="line" lang="c">    <span class="n" style="color: #333;">g_ld_window_r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">ldip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">window_r2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5868" 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">

5868

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<pre style="margin: 0;"> <span id="LC5868" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5867" 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">

5867

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<td class="diff-line-num new_line" data-linenumber="5869" 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">

5869

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<pre style="margin: 0;"> <span id="LC5869" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ld_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">LD_DX</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5868" 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">

5868

</td>

<td class="diff-line-num new_line" data-linenumber="5870" 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">

5870

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5870" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// this is more like --fast-epistasis under the hood, since it requires the</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10535" 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="10537" 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">@@ -10535,7 +10537,7 @@ int32_t indep_pairphase(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uint</td>

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<td class="diff-line-num old_line" data-linenumber="10535" 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">

10535

</td>

<td class="diff-line-num new_line" data-linenumber="10537" 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">

10537

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10537" class="line" lang="c">    <span class="n" style="color: #333;">geno</span><span class="p">[</span><span class="n" style="color: #333;">ulii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">founder_ctsplit</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="n" style="color: #333;">founder_ctv3</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;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10536" 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">

10536

</td>

<td class="diff-line-num new_line" data-linenumber="10538" 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">

10538

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10538" class="line" lang="c">    <span class="n" style="color: #333;">geno</span><span class="p">[</span><span class="n" style="color: #333;">ulii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">founder_ctsplit</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">founder_ctsplit</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;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10537" 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">

10537

</td>

<td class="diff-line-num new_line" data-linenumber="10539" 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">

10539

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10539" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10538" 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">

10538

</td>

<td class="diff-line-num new_line old" data-linenumber="10540" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10538" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="10539" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10540" 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">

10540

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10540" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">]))</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10539" 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">

10539

</td>

<td class="diff-line-num new_line" data-linenumber="10541" 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">

10541

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10541" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_ul</span><span class="p">(</span><span class="n" style="color: #333;">founder_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_male_collapsed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10540" 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">

10540

</td>

<td class="diff-line-num new_line" data-linenumber="10542" 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">

10542

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10542" class="line" lang="c">        <span class="n" style="color: #333;">bigstack_alloc_ul</span><span class="p">(</span><span class="n" style="color: #333;">founder_ctsplit</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_geno1_male</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="10541" 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">

10541

</td>

<td class="diff-line-num new_line" data-linenumber="10543" 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">

10543

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10543" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">indep_pairphase_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="ad63a8112365845088935bd1cf043fd5464ed840">

<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/263450c4600d065fa2b4be097fa9732be028cbfe...fc42abb3dfb33ccca769c6efc3bd453215e89b4f#ad63a8112365845088935bd1cf043fd5464ed840"><strong>plink_misc.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2444" 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="2444" 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">@@ -2444,7 +2444,7 @@ int32_t write_stratified_freqs(FILE* bedfile, uintptr_t bed_offset, char* outnam</td>

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<td class="diff-line-num old_line" data-linenumber="2444" 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">

2444

</td>

<td class="diff-line-num new_line" data-linenumber="2444" 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">

2444

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<pre style="margin: 0;"> <span id="LC2444" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2445" 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">

2445

</td>

<td class="diff-line-num new_line" data-linenumber="2445" 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">

2445

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2445" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2446" 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">

2446

</td>

<td class="diff-line-num new_line" data-linenumber="2446" 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">

2446

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2446" class="line" lang="c">  <span class="n" style="color: #333;">chrom_idx</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">X_OFFSET</span><span class="p">];</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2447" 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">

2447

</td>

<td class="diff-line-num new_line old" data-linenumber="2447" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2447" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2448" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2447" 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">

2447

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2447" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2448" 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">

2448

</td>

<td class="diff-line-num new_line" data-linenumber="2448" 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">

2448

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2448" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_ui</span><span class="p">(</span><span class="n" style="color: #333;">cluster_ct</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;">cluster_starts_nonmale</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2449" 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">

2449

</td>

<td class="diff-line-num new_line" data-linenumber="2449" 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">

2449

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2449" class="line" lang="c">        <span class="n" style="color: #333;">bigstack_alloc_ui</span><span class="p">(</span><span class="n" style="color: #333;">sample_f_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sample_f_male_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cluster_map_nonmale</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2450" 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">

2450

</td>

<td class="diff-line-num new_line" data-linenumber="2450" 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">

2450

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2450" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">write_stratified_freqs_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2464" 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="2464" 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">@@ -2464,7 +2464,7 @@ int32_t write_stratified_freqs(FILE* bedfile, uintptr_t bed_offset, char* outnam</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2464" 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">

2464

</td>

<td class="diff-line-num new_line" data-linenumber="2464" 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">

2464

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2464" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2465" 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">

2465

</td>

<td class="diff-line-num new_line" data-linenumber="2465" 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">

2465

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2465" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2466" 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">

2466

</td>

<td class="diff-line-num new_line" data-linenumber="2466" 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">

2466

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2466" class="line" lang="c">  <span class="n" style="color: #333;">chrom_idx</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;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">Y_OFFSET</span><span class="p">];</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2467" 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">

2467

</td>

<td class="diff-line-num new_line old" data-linenumber="2467" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2467" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cluster_map_nonmale</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2468" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2467" 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">

2467

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2467" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cluster_map_nonmale</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2468" 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">

2468

</td>

<td class="diff-line-num new_line" data-linenumber="2468" 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">

2468

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2468" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_ui</span><span class="p">(</span><span class="n" style="color: #333;">cluster_ct</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;">cluster_starts_male</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2469" 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">

2469

</td>

<td class="diff-line-num new_line" data-linenumber="2469" 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">

2469

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2469" class="line" lang="c">        <span class="n" style="color: #333;">bigstack_alloc_ui</span><span class="p">(</span><span class="n" style="color: #333;">sample_f_male_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cluster_map_male</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2470" 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">

2470

</td>

<td class="diff-line-num new_line" data-linenumber="2470" 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">

2470

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2470" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">write_stratified_freqs_ret_NOMEM</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3067" 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="3067" 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">@@ -3067,7 +3067,7 @@ int32_t sexcheck(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3067" 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">

3067

</td>

<td class="diff-line-num new_line" data-linenumber="3067" 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">

3067

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3067" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3068" 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">

3068

</td>

<td class="diff-line-num new_line" data-linenumber="3068" 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">

3068

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3068" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3069" 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">

3069

</td>

<td class="diff-line-num new_line" data-linenumber="3069" 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">

3069

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3069" 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;">yonly</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3070" 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">

3070

</td>

<td class="diff-line-num new_line old" data-linenumber="3070" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3070" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></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;">is_set</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;">chrom_mask</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;">x_code</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3071" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3070" 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">

3070

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3070" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">x_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></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;">is_set</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;">chrom_mask</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;">x_code</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3071" 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">

3071

</td>

<td class="diff-line-num new_line" data-linenumber="3071" 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">

3071

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3071" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">sexcheck_ret_NO_X_VAR</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3072" 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">

3072

</td>

<td class="diff-line-num new_line" data-linenumber="3072" 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">

3072

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3072" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3073" 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">

3073

</td>

<td class="diff-line-num new_line" data-linenumber="3073" 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">

3073

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3073" class="line" lang="c">    <span class="n" style="color: #333;">marker_uidx_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_chrom_end_vidx</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</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;">x_code</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3134" 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="3134" 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">@@ -3134,7 +3134,7 @@ int32_t sexcheck(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outna</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3134" 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">

3134

</td>

<td class="diff-line-num new_line" data-linenumber="3134" 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">

3134

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3134" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3135" 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">

3135

</td>

<td class="diff-line-num new_line" data-linenumber="3135" 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">

3135

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3135" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3136" 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">

3136

</td>

<td class="diff-line-num new_line" data-linenumber="3136" 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">

3136

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3136" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_y</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3137" 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">

3137

</td>

<td class="diff-line-num new_line old" data-linenumber="3137" 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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3137" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">y_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3138" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3137" 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">

3137

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3137" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_set</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;">chrom_mask</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;">y_code</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3138" 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">

3138

</td>

<td class="diff-line-num new_line" data-linenumber="3138" 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">

3138

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3138" class="line" lang="c">      <span class="n" style="color: #333;">marker_uidx_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_chrom_end_vidx</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</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;">y_code</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3139" 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">

3139

</td>

<td class="diff-line-num new_line" data-linenumber="3139" 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">

3139

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3139" class="line" lang="c">      <span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_unset_ul</span><span class="p">(</span><span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">get_chrom_start_vidx</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</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;">y_code</span><span class="p">),</span> <span class="n" style="color: #333;">marker_uidx_end</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="3140" 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">

3140

</td>

<td class="diff-line-num new_line" data-linenumber="3140" 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">

3140

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3140" class="line" lang="c">      <span class="n" style="color: #333;">ytotal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker_uidx_end</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="n" style="color: #333;">popcount_bit_idx</span><span class="p">(</span><span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">marker_uidx</span><span class="p">,</span> <span class="n" style="color: #333;">marker_uidx_end</span><span class="p">);</span></span>

</pre>

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