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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/2aaa4872560daa25e2010f56b88dbad02cf67fc6">2aaa4872</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-03-27T08:42:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-200321+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c">a4645c27</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-03-27T08:42:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.00_a3-200321+dfsg'
Update to upstream version '2.00~a3-200321+dfsg'
with Debian dir faa206c1e1fc7820c0e8b7c4974ea5eab3013df9</pre>
</li>
</ul>
<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#386f23c017c84fb5b75ce96dbac305abca500153">
include/pgenlib_misc.cc
</a>
</li>
<li class="file-stats">
<a href="#e77f6102ff6675b5bc8947f913bdad39d3e254f4">
include/pgenlib_misc.h
</a>
</li>
<li class="file-stats">
<a href="#4776c94d0e4a55582487ac9c960d27e25dcb2101">
include/pgenlib_read.cc
</a>
</li>
<li class="file-stats">
<a href="#5fce52c5aa6c7bce70dfbc7bf69033d4e1b69e50">
include/plink2_base.cc
</a>
</li>
<li class="file-stats">
<a href="#f2695700d4614304f2acf05f9546dcf4b3608c47">
include/plink2_base.h
</a>
</li>
<li class="file-stats">
<a href="#df87a656e39e60d062ab0047bd78b5260a146504">
include/plink2_bits.cc
</a>
</li>
<li class="file-stats">
<a href="#b294a1a5c458bca5a817f674d97272b064975c1a">
include/plink2_bits.h
</a>
</li>
<li class="file-stats">
<a href="#4b320ace526dc39d7e8f303b1481e411020379dc">
include/plink2_string.cc
</a>
</li>
<li class="file-stats">
<a href="#e04ad6b4524c358c1efeb53be9496b769cc2fe19">
include/plink2_string.h
</a>
</li>
<li class="file-stats">
<a href="#21867eb3deeaf9db3872b9470e5dd6366a2591cf">
pgenlibr/src/Makevars
</a>
</li>
<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
</a>
</li>
<li class="file-stats">
<a href="#5c0ac48ba397674ac28142efc3b29b7de442d076">
plink2_cmdline.cc
</a>
</li>
<li class="file-stats">
<a href="#353424a9b88ab7aad403c3734bdd60f28af6b661">
plink2_cmdline.h
</a>
</li>
<li class="file-stats">
<a href="#8abb94ca0fef8a58740274abf79b38fd70201601">
plink2_common.cc
</a>
</li>
<li class="file-stats">
<a href="#576e4fd14d1d66b779bb9f5d05d29f2871392d1a">
plink2_common.h
</a>
</li>
<li class="file-stats">
<a href="#49a9b8ad832d31a64af7997ab4dff296fe4603bc">
plink2_data.cc
</a>
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<li class="file-stats">
<a href="#a125279a9188813c60a6fe3d56cead0bd36fcc8f">
plink2_data.h
</a>
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<li class="file-stats">
<a href="#a1236d7e51efdf6705792595d24aa915967b7759">
plink2_decompress.h
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<li class="file-stats">
<a href="#0bb44e45468b97ef0c21ed5ca6767a690fbf6626">
plink2_export.cc
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</li>
<li class="file-stats">
<a href="#6414bd7aa55c6eef0319abf2a95e1f61296d37e8">
plink2_export.h
</a>
</li>
<li class="file-stats">
<a href="#54428596f28c10964056a17b50b54e463f1f7362">
plink2_filter.cc
</a>
</li>
<li class="file-stats">
<a href="#82c8c0946825d16815c68e845955a90079d70b6b">
plink2_glm.cc
</a>
</li>
<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
</a>
</li>
<li class="file-stats">
<a href="#21274e2b169d6e71a254a974b86ae7af8acdf275">
plink2_import.cc
</a>
</li>
<li class="file-stats">
<a href="#d029425224aa0cc89613ddc5656608ce6488e765">
plink2_import.h
</a>
</li>
<li class="file-stats">
<a href="#f5d85292088358ebd24c2a15cd3a9b7759ba61c9">
plink2_matrix.h
</a>
</li>
<li class="file-stats">
<a href="#9e0620cca890479e38d176e292c73012d6b0f630">
plink2_matrix_calc.cc
</a>
</li>
<li class="file-stats">
<a href="#112cb73bff359b837852d2266ec756df9e6637d8">
plink2_pvar.cc
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="386f23c017c84fb5b75ce96dbac305abca500153">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#386f23c017c84fb5b75ce96dbac305abca500153"><strong>include/pgenlib_misc.cc</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1181" style="width: 35px; color: rgba(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">@@ -1181,12 +1181,12 @@ void TransposeNypblock64(const uintptr_t* read_iter, uint32_t read_ul_stride, ui</td>
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1181
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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1182
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1182
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo16</span><span class="p">(</span><span class="n" style="color: #333;">loader0</span><span class="p">,</span> <span class="n" style="color: #333;">loader1</span><span class="p">);</span></span>
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1183
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<td class="diff-line-num new_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi16</span><span class="p">(</span><span class="n" style="color: #333;">loader0</span><span class="p">,</span> <span class="n" style="color: #333;">loader1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1184" 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">
1184
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<td class="diff-line-num new_line old" data-linenumber="1184" 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="LC1184" class="line" lang="cpp"> <span class="n" style="color: #333;">loader0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m16</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m16</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1185" 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">
1185
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<pre style="margin: 0;">-<span id="LC1185" class="line" lang="cpp"> <span class="n" style="color: #333;">loader1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</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">m16</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m16</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1186" 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="LC1184" class="line" lang="cpp"> <span class="n" style="color: #333;">loader0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m16</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1185" 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="LC1185" class="line" lang="cpp"> <span class="n" style="color: #333;">loader1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m16</span></span><span class="p">);</span></span>
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1186
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo16</span><span class="p">(</span><span class="n" style="color: #333;">loader2</span><span class="p">,</span> <span class="n" style="color: #333;">loader3</span><span class="p">);</span></span>
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1187
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1187
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi16</span><span class="p">(</span><span class="n" style="color: #333;">loader2</span><span class="p">,</span> <span class="n" style="color: #333;">loader3</span><span class="p">);</span></span>
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1188
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="cpp"> <span class="n" style="color: #333;">loader2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m16</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m16</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="cpp"> <span class="n" style="color: #333;">loader3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</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">m16</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m16</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="cpp"> <span class="n" style="color: #333;">loader2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m16</span></span><span class="p">);</span></span>
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1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp"> <span class="n" style="color: #333;">loader3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">16</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m16</span></span><span class="p">);</span></span>
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1190
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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1191
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (0,0) (0,1) (1,0) ... (7,1) (0,2) ... (7,3) (8,0) ... (31,3)</span></span>
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1192
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1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// + (0,4) ... (31,7)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1232" style="width: 35px; color: rgba(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="1232" style="width: 35px; color: rgba(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">@@ -1232,7 +1232,7 @@ void TransposeNypblock64(const uintptr_t* read_iter, uint32_t read_ul_stride, ui</td>
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1232
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1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and target_4567 to</span></span>
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1233
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1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// _ (4, 0) _ (5, 0) _ (6, 0) _ (7, 0) _ (4, 1) _ (5, 1) _ (6, 1) ...</span></span>
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1234
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1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This is perfectly arranged for movemask.</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_4567</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</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">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">loader</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_4567</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">7</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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1236
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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter7</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">);</span></span>
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1237
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1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="cpp"> <span class="n" style="color: #333;">target_4567</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_slli</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1238
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1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter6</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1240" style="width: 35px; color: rgba(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">@@ -1240,7 +1240,7 @@ void TransposeNypblock64(const uintptr_t* read_iter, uint32_t read_ul_stride, ui</td>
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter5</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">);</span></span>
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"> <span class="n" style="color: #333;">target_4567</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_slli</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter4</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_4567</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </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="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter3</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">);</span></span>
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1245
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="cpp"> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_slli</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1246
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter2</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1260,7 +1260,7 @@ void TransposeNypblock64(const uintptr_t* read_iter, uint32_t read_ul_stride, ui</td>
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1260
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1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="cpp"> <span class="n" style="color: #333;">Vec8thUint</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target_iter3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">target_iter2</span><span class="p">[</span><span class="n" style="color: #333;">write_v8ui_stride</span><span class="p">]);</span></span>
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1261
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1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="cpp"> <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;">vidx</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;">vidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vec_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vidx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">loader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_iter</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">];</span></span>
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1263
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<pre style="margin: 0;">-<span id="LC1263" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </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="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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1264
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1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter3</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">);</span></span>
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1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="cpp"> <span class="n" style="color: #333;">target_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_slli</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp"> <span class="n" style="color: #333;">target_iter2</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_movemask</span><span class="p">(</span><span class="n" style="color: #333;">target_0123</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1420,8 +1420,9 @@ void SplitHomRef2het(const uintptr_t* genoarr, uint32_t sample_ct, uintptr_t* __</td>
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="cpp"> <span class="p">}</span></span>
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1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="cpp"><span class="p">}</span></span>
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1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1423" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1424" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Note that once the result elements are only 4 bits wide, shuffle8 should</span></span>
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// beat a 256x4 lookup table when SSE4 is available. (possible todo: see if</span></span>
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// shuffle8-based loop also wins here.)</span></span>
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1426
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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrLookup256x1bx4</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">genoarr_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">genoarr</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1440" style="width: 35px; color: rgba(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">@@ -1440,7 +1441,6 @@ void GenoarrLookup256x1bx4(const uintptr_t* genoarr, const void* table256x1bx4,</td>
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1443" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrLookup16x4bx2</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table16x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table16x4bx2</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1666,6 +1666,54 @@ void InitLookup16x8bx2(void* table16x8bx2) {</td>
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="cpp"> <span class="p">}</span></span>
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1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="cpp"><span class="p">}</span></span>
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1668
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1668
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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="cpp"></span>
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1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x1bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">)</span> <span class="p">{</span></span>
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1670
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<pre style="margin: 0;">+<span id="LC1670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">);</span></span>
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1671
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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1672
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">];</span></span>
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1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">];</span></span>
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1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1677
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<pre style="margin: 0;">+<span id="LC1677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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1678
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<pre style="margin: 0;">+<span id="LC1678" class="line" lang="cpp"> <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;">second_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;">second_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">second_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">second_idx</span><span class="p">];</span></span>
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1680
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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="cpp"> <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;">third_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;">third_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">third_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1681
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<pre style="margin: 0;">+<span id="LC1681" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_third</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">third_idx</span><span class="p">];</span></span>
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1682
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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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1684
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<pre style="margin: 0;">+<span id="LC1684" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_third</span><span class="p">;</span></span>
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1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_second</span><span class="p">;</span></span>
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1686
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="cpp"> <span class="p">}</span></span>
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1688
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="cpp"> <span class="p">}</span></span>
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1689
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="cpp"> <span class="p">}</span></span>
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1690
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="cpp"> <span class="p">}</span></span>
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1691
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<pre style="margin: 0;">+<span id="LC1691" class="line" lang="cpp"><span class="p">}</span></span>
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1692
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="cpp"></span>
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1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x2bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x2bx4</span><span class="p">)</span> <span class="p">{</span></span>
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1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table256x2bx4</span><span class="p">);</span></span>
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1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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1696
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<pre style="margin: 0;">+<span id="LC1696" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">];</span></span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">];</span></span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1701
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<pre style="margin: 0;">+<span id="LC1701" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="cpp"> <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;">second_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;">second_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">second_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">second_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1704" 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">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="cpp"> <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;">third_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;">third_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">third_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_third</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">third_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1706" 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">
1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1707" 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">
1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1708" 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">
1708
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_third</span><span class="p">;</span></span>
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1709
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_second</span><span class="p">;</span></span>
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="cpp"> <span class="p">}</span></span>
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1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="cpp"> <span class="p">}</span></span>
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1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="cpp"> <span class="p">}</span></span>
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1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="cpp"> <span class="p">}</span></span>
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1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="cpp"><span class="p">}</span></span>
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1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="cpp"></span>
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1669
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1717
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<pre style="margin: 0;"> <span id="LC1717" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x4bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x4bx4</span><span class="p">)</span> <span class="p">{</span></span>
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1670
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1718
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<pre style="margin: 0;"> <span id="LC1718" class="line" lang="cpp"> <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;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table256x4bx4</span><span class="p">);</span></span>
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1671
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1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1798" style="width: 35px; color: rgba(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="1846" style="width: 35px; color: rgba(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">@@ -1798,6 +1846,158 @@ void InitPhaseLookup4b(void* table56x4bx2) {</td>
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1798
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1846
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="cpp"> <span class="p">}</span></span>
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1799
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1847
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<pre style="margin: 0;"> <span id="LC1847" class="line" lang="cpp"><span class="p">}</span></span>
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1800
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1848
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<pre style="margin: 0;"> <span id="LC1848" class="line" lang="cpp"></span>
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1849
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<pre style="margin: 0;">+<span id="LC1849" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LP64__</span></span>
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1850
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<pre style="margin: 0;">+<span id="LC1850" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PhaseLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phasepresent</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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1851
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<pre style="margin: 0;">+<span id="LC1851" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">);</span></span>
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1852
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<pre style="margin: 0;">+<span id="LC1852" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1853" 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">
1853
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<pre style="margin: 0;">+<span id="LC1853" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phasepresent_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">);</span></span>
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1854
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<pre style="margin: 0;">+<span id="LC1854" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phaseinfo_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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1855
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<pre style="margin: 0;">+<span id="LC1855" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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1857
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<pre style="margin: 0;">+<span id="LC1857" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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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1858
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<pre style="margin: 0;">+<span id="LC1858" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phasepresent_hw_shifted</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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1859
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<pre style="margin: 0;">+<span id="LC1859" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</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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1860
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<pre style="margin: 0;">+<span id="LC1860" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1861" 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">
1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1862" 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">
1862
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<pre style="margin: 0;">+<span id="LC1862" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1863" 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">
1863
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<pre style="margin: 0;">+<span id="LC1863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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1864
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<pre style="margin: 0;">+<span id="LC1864" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</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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1865
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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1866
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<pre style="margin: 0;">+<span id="LC1866" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1867
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<pre style="margin: 0;">+<span id="LC1867" class="line" lang="cpp"> <span class="p">}</span></span>
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1868
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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">]),</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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1869
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<pre style="margin: 0;">+<span id="LC1869" class="line" lang="cpp"> <span class="p">}</span></span>
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1870
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<pre style="margin: 0;">+<span id="LC1870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1871
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<pre style="margin: 0;">+<span id="LC1871" class="line" lang="cpp"> <span class="p">}</span></span>
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1872
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<pre style="margin: 0;">+<span id="LC1872" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1873
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<pre style="margin: 0;">+<span id="LC1873" class="line" lang="cpp"> <span class="p">}</span></span>
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1874
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<pre style="margin: 0;">+<span id="LC1874" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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1875
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<pre style="margin: 0;">+<span id="LC1875" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasepresent_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1876" 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">
1876
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<pre style="margin: 0;">+<span id="LC1876" class="line" lang="cpp"> <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;">phasepresent_hw_shifted</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1877" 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">
1877
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<pre style="margin: 0;">+<span id="LC1877" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1878" 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">
1878
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<pre style="margin: 0;">+<span id="LC1878" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">]);</span></span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">result_iter</span><span class="p">;</span></span>
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1880
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<pre style="margin: 0;">+<span id="LC1880" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1881
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<pre style="margin: 0;">+<span id="LC1881" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1882" 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">
1882
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<pre style="margin: 0;">+<span id="LC1882" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1883
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<pre style="margin: 0;">+<span id="LC1883" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1884" 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">
1884
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<pre style="margin: 0;">+<span id="LC1884" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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1885
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<pre style="margin: 0;">+<span id="LC1885" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1886
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<pre style="margin: 0;">+<span id="LC1886" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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1887
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<pre style="margin: 0;">+<span id="LC1887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">))</span> <span class="o" style="font-weight: 600;">^</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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1888
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<pre style="margin: 0;">+<span id="LC1888" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">]);</span></span>
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1889
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<pre style="margin: 0;">+<span id="LC1889" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">result_iter</span><span class="p">;</span></span>
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1890
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<pre style="margin: 0;">+<span id="LC1890" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1891
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<pre style="margin: 0;">+<span id="LC1891" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1892
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<pre style="margin: 0;">+<span id="LC1892" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1893
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<pre style="margin: 0;">+<span id="LC1893" class="line" lang="cpp"> <span class="p">}</span></span>
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1894
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<pre style="margin: 0;">+<span id="LC1894" class="line" lang="cpp"> <span class="p">}</span></span>
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1895
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<pre style="margin: 0;">+<span id="LC1895" class="line" lang="cpp"> <span class="p">}</span></span>
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1896
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<pre style="margin: 0;">+<span id="LC1896" class="line" lang="cpp"><span class="p">}</span></span>
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1897
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<pre style="margin: 0;">+<span id="LC1897" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PhaseLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phasepresent</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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1899
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<pre style="margin: 0;">+<span id="LC1899" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">);</span></span>
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1900
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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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1901
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<pre style="margin: 0;">+<span id="LC1901" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phasepresent_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">);</span></span>
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1902
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<pre style="margin: 0;">+<span id="LC1902" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phaseinfo_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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1903
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<pre style="margin: 0;">+<span id="LC1903" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1904" 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">
1904
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<pre style="margin: 0;">+<span id="LC1904" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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1905
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<pre style="margin: 0;">+<span id="LC1905" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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 new_line" data-linenumber="1906" 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">
1906
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<pre style="margin: 0;">+<span id="LC1906" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phasepresent_hw_shifted</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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1907
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<pre style="margin: 0;">+<span id="LC1907" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</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 new_line" data-linenumber="1908" 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">
1908
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<pre style="margin: 0;">+<span id="LC1908" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1909" 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">
1909
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<pre style="margin: 0;">+<span id="LC1909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1910" 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">
1910
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<pre style="margin: 0;">+<span id="LC1910" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1911" 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">
1911
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<pre style="margin: 0;">+<span id="LC1911" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1912" 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">
1912
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<pre style="margin: 0;">+<span id="LC1912" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</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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<td class="diff-line-num new new_line" data-linenumber="1913" 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">
1913
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<pre style="margin: 0;">+<span id="LC1913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1914" 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">
1914
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<pre style="margin: 0;">+<span id="LC1914" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">^=</span> <span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1915" 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">
1915
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<pre style="margin: 0;">+<span id="LC1915" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1916" 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">
1916
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<pre style="margin: 0;">+<span id="LC1916" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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1917
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<pre style="margin: 0;">+<span id="LC1917" class="line" lang="cpp"> <span class="p">}</span></span>
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1918
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<pre style="margin: 0;">+<span id="LC1918" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1919" 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">
1919
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<pre style="margin: 0;">+<span id="LC1919" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1920" 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">
1920
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<pre style="margin: 0;">+<span id="LC1920" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1921" 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">
1921
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<pre style="margin: 0;">+<span id="LC1921" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1922" 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">
1922
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<pre style="margin: 0;">+<span id="LC1922" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1923" 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">
1923
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<pre style="margin: 0;">+<span id="LC1923" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasepresent_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1924" 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">
1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="cpp"> <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;">phasepresent_hw_shifted</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1925" 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">
1925
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<pre style="margin: 0;">+<span id="LC1925" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1927" 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">
1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="cpp"> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="cpp"> <span class="p">}</span></span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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1933
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<pre style="margin: 0;">+<span id="LC1933" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1934
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<pre style="margin: 0;">+<span id="LC1934" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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1935
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<pre style="margin: 0;">+<span id="LC1935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">))</span> <span class="o" style="font-weight: 600;">^</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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1936
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<pre style="margin: 0;">+<span id="LC1936" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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1937
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<pre style="margin: 0;">+<span id="LC1937" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="cpp"> <span class="n" style="color: #333;">phasepresent_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1940
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<pre style="margin: 0;">+<span id="LC1940" class="line" lang="cpp"> <span class="p">}</span></span>
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1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="cpp"> <span class="p">}</span></span>
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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="cpp"> <span class="p">}</span></span>
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1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="cpp"><span class="p">}</span></span>
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1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="cpp"></span>
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1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitPhaseLookup8b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">)</span> <span class="p">{</span></span>
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1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">);</span></span>
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1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1950
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<pre style="margin: 0;">+<span id="LC1950" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1951
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<pre style="margin: 0;">+<span id="LC1951" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1952" 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">
1952
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<pre style="margin: 0;">+<span id="LC1952" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1953
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<pre style="margin: 0;">+<span id="LC1953" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1954" 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">
1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1957" 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">
1957
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<pre style="margin: 0;">+<span id="LC1957" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1958" 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">
1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1959
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<pre style="margin: 0;">+<span id="LC1959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1960" 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">
1960
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<pre style="margin: 0;">+<span id="LC1960" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1961
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<pre style="margin: 0;">+<span id="LC1961" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1962" 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">
1962
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<pre style="margin: 0;">+<span id="LC1962" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="cpp"> <span class="p">}</span></span>
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1964
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<pre style="margin: 0;">+<span id="LC1964" class="line" lang="cpp"> <span class="p">}</span></span>
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1965
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<pre style="margin: 0;">+<span id="LC1965" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [16][0]..[31][1]: bit 4 is set</span></span>
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1966
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<pre style="margin: 0;">+<span id="LC1966" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// low bits must be 01 or 11</span></span>
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1967
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<pre style="margin: 0;">+<span id="LC1967" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">val_phaseinfo0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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1968
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<pre style="margin: 0;">+<span id="LC1968" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1969
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<pre style="margin: 0;">+<span id="LC1969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">val_phaseinfo1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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1970
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<pre style="margin: 0;">+<span id="LC1970" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1971" 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">
1971
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<pre style="margin: 0;">+<span id="LC1971" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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1972
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<pre style="margin: 0;">+<span id="LC1972" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_phaseinfo0</span><span class="p">;</span></span>
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1975
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<pre style="margin: 0;">+<span id="LC1975" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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1976
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<pre style="margin: 0;">+<span id="LC1976" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_phaseinfo1</span><span class="p">;</span></span>
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1977
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<pre style="margin: 0;">+<span id="LC1977" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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1978
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<pre style="margin: 0;">+<span id="LC1978" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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1979
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<pre style="margin: 0;">+<span id="LC1979" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1980" 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">
1980
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<pre style="margin: 0;">+<span id="LC1980" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [32][0]..[39][1]: bit 5 set, bit 4 unset</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1981" 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">
1981
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<pre style="margin: 0;">+<span id="LC1981" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// high bits must be 00 or 01</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1982" 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">
1982
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<pre style="margin: 0;">+<span id="LC1982" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1983" 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">
1983
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<pre style="margin: 0;">+<span id="LC1983" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_idx</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">val_phaseinfo0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">val_phaseinfo1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1984" 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">
1984
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<pre style="margin: 0;">+<span id="LC1984" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1985" 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">
1985
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<pre style="margin: 0;">+<span id="LC1985" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1986" 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">
1986
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<pre style="margin: 0;">+<span id="LC1986" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1987" 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">
1987
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<pre style="margin: 0;">+<span id="LC1987" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1988" 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">
1988
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<pre style="margin: 0;">+<span id="LC1988" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1989" 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">
1989
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<pre style="margin: 0;">+<span id="LC1989" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1990" 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">
1990
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<pre style="margin: 0;">+<span id="LC1990" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [48][0]..[55][1]: bits 4 and 5 set</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1991" 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">
1991
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<pre style="margin: 0;">+<span id="LC1991" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1992" 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">
1992
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<pre style="margin: 0;">+<span id="LC1992" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">high_idx</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">val_phaseinfo0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">val_phaseinfo1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1993" 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">
1993
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<pre style="margin: 0;">+<span id="LC1993" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_phaseinfo0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1994" 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">
1994
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<pre style="margin: 0;">+<span id="LC1994" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1995" 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">
1995
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<pre style="margin: 0;">+<span id="LC1995" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_phaseinfo1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1996" 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">
1996
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<pre style="margin: 0;">+<span id="LC1996" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1997" 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">
1997
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<pre style="margin: 0;">+<span id="LC1997" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1998" 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">
1998
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<pre style="margin: 0;">+<span id="LC1998" class="line" lang="cpp"> <span class="p">}</span></span>
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1999
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<pre style="margin: 0;">+<span id="LC1999" class="line" lang="cpp"><span class="p">}</span></span>
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2000
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<pre style="margin: 0;">+<span id="LC2000" class="line" lang="cpp"></span>
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1801
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2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bits 0..3: two genotypes</span></span>
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1802
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2002
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<pre style="margin: 0;"> <span id="LC2002" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bits 4..5: two (phasepresent | sex_male) bits</span></span>
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<td class="diff-line-num old_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1803
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2003
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<pre style="margin: 0;"> <span id="LC2003" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bits 1,3: unpacked phaseinfo xor</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1925" style="width: 35px; color: rgba(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="2125" style="width: 35px; color: rgba(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">@@ -1925,6 +2125,393 @@ void GenoarrSexLookup4b(const uintptr_t* genoarr, const uintptr_t* sex_male, con</td>
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1925
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2125
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<pre style="margin: 0;"> <span id="LC2125" class="line" lang="cpp"> <span class="p">}</span></span>
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1926
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2126
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<pre style="margin: 0;"> <span id="LC2126" class="line" lang="cpp"><span class="p">}</span></span>
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1927
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2127
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<pre style="margin: 0;"> <span id="LC2127" class="line" lang="cpp"></span>
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2128
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<pre style="margin: 0;">+<span id="LC2128" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitPhaseXNohhLookup8b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">)</span> <span class="p">{</span></span>
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2129
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<pre style="margin: 0;">+<span id="LC2129" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">);</span></span>
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2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="cpp"> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2141
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<pre style="margin: 0;">+<span id="LC2141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2143
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<pre style="margin: 0;">+<span id="LC2143" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="cpp"> <span class="p">}</span></span>
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2146
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<pre style="margin: 0;">+<span id="LC2146" class="line" lang="cpp"> <span class="p">}</span></span>
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2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [16][0]..[31][1]: bit 4 is set</span></span>
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2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2150
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<pre style="margin: 0;">+<span id="LC2150" class="line" lang="cpp"> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2152
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="cpp"> <span class="p">}</span></span>
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2153
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<pre style="margin: 0;">+<span id="LC2153" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2154
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<pre style="margin: 0;">+<span id="LC2154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2156
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<pre style="margin: 0;">+<span id="LC2156" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2157
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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2158
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="cpp"> <span class="p">}</span></span>
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2159
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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="cpp"> <span class="p">}</span></span>
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2160
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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [32][0]..[47][1]: bit 5 set, bit 4 unset</span></span>
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2161
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<pre style="margin: 0;">+<span id="LC2161" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2162
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<pre style="margin: 0;">+<span id="LC2162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2163
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<pre style="margin: 0;">+<span id="LC2163" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2164
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<pre style="margin: 0;">+<span id="LC2164" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2165
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<pre style="margin: 0;">+<span id="LC2165" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2166
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<pre style="margin: 0;">+<span id="LC2166" class="line" lang="cpp"> <span class="p">}</span></span>
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2167
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<pre style="margin: 0;">+<span id="LC2167" class="line" lang="cpp"> <span class="p">}</span></span>
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2168
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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [48][0]..[63][1]: bits 4 and 5 set</span></span>
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2169
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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2170
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<pre style="margin: 0;">+<span id="LC2170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2171
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<pre style="margin: 0;">+<span id="LC2171" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2172
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<pre style="margin: 0;">+<span id="LC2172" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">male_or_phasepresent_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2173
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<pre style="margin: 0;">+<span id="LC2173" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2174
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<pre style="margin: 0;">+<span id="LC2174" class="line" lang="cpp"> <span class="p">}</span></span>
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2175
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<pre style="margin: 0;">+<span id="LC2175" class="line" lang="cpp"> <span class="p">}</span></span>
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2176
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<pre style="margin: 0;">+<span id="LC2176" class="line" lang="cpp"><span class="p">}</span></span>
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2177
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<pre style="margin: 0;">+<span id="LC2177" class="line" lang="cpp"></span>
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2178
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<pre style="margin: 0;">+<span id="LC2178" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LP64__</span></span>
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2179
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<pre style="margin: 0;">+<span id="LC2179" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrSexLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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2180
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<pre style="margin: 0;">+<span id="LC2180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">);</span></span>
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2181
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<pre style="margin: 0;">+<span id="LC2181" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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2182
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<pre style="margin: 0;">+<span id="LC2182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">);</span></span>
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2183
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<pre style="margin: 0;">+<span id="LC2183" class="line" lang="cpp"> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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2184
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<pre style="margin: 0;">+<span id="LC2184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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2185
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<pre style="margin: 0;">+<span id="LC2185" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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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2186
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<pre style="margin: 0;">+<span id="LC2186" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">male_hw_shifted</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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2187
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<pre style="margin: 0;">+<span id="LC2187" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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2188
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<pre style="margin: 0;">+<span id="LC2188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2189" 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">
2189
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<pre style="margin: 0;">+<span id="LC2189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2190" 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">
2190
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<pre style="margin: 0;">+<span id="LC2190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2191
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<pre style="margin: 0;">+<span id="LC2191" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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2192
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<pre style="margin: 0;">+<span id="LC2192" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">]),</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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2193
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<pre style="margin: 0;">+<span id="LC2193" class="line" lang="cpp"> <span class="p">}</span></span>
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2194
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<pre style="margin: 0;">+<span id="LC2194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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2195
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<pre style="margin: 0;">+<span id="LC2195" class="line" lang="cpp"> <span class="p">}</span></span>
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2196
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<pre style="margin: 0;">+<span id="LC2196" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2197
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<pre style="margin: 0;">+<span id="LC2197" class="line" lang="cpp"> <span class="p">}</span></span>
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2198
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<pre style="margin: 0;">+<span id="LC2198" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sex_male_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2200
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;"><<=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2202
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<pre style="margin: 0;">+<span id="LC2202" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">)]);</span></span>
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2203
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<pre style="margin: 0;">+<span id="LC2203" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">result_iter</span><span class="p">;</span></span>
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2204
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<pre style="margin: 0;">+<span id="LC2204" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2206
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<pre style="margin: 0;">+<span id="LC2206" class="line" lang="cpp"> <span class="p">}</span></span>
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2207
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<pre style="margin: 0;">+<span id="LC2207" class="line" lang="cpp"> <span class="p">}</span></span>
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2208
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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="cpp"><span class="p">}</span></span>
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2209
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<pre style="margin: 0;">+<span id="LC2209" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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2210
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<pre style="margin: 0;">+<span id="LC2210" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrSexLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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2211
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<pre style="margin: 0;">+<span id="LC2211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">);</span></span>
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2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2213" 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">
2213
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<pre style="margin: 0;">+<span id="LC2213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">);</span></span>
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2214
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<pre style="margin: 0;">+<span id="LC2214" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2215" 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">
2215
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<pre style="margin: 0;">+<span id="LC2215" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2216" 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">
2216
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<pre style="margin: 0;">+<span id="LC2216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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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2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">male_hw_shifted</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 new_line" data-linenumber="2218" 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">
2218
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<pre style="margin: 0;">+<span id="LC2218" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2219" 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">
2219
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<pre style="margin: 0;">+<span id="LC2219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2220" 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">
2220
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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2221" 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">
2221
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<pre style="margin: 0;">+<span id="LC2221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2222
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<pre style="margin: 0;">+<span id="LC2222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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2223
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<pre style="margin: 0;">+<span id="LC2223" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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2224
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<pre style="margin: 0;">+<span id="LC2224" class="line" lang="cpp"> <span class="p">}</span></span>
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2225
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<pre style="margin: 0;">+<span id="LC2225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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2226
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2227" 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">
2227
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<pre style="margin: 0;">+<span id="LC2227" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2228
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<pre style="margin: 0;">+<span id="LC2228" class="line" lang="cpp"> <span class="p">}</span></span>
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2229
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<pre style="margin: 0;">+<span id="LC2229" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2230
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<pre style="margin: 0;">+<span id="LC2230" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sex_male_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2231
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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;"><<=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2232
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<pre style="margin: 0;">+<span id="LC2232" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2233
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<pre style="margin: 0;">+<span id="LC2233" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[((</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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2234
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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="cpp"> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2235
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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2236
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<pre style="margin: 0;">+<span id="LC2236" class="line" lang="cpp"> <span class="n" style="color: #333;">male_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2237
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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="cpp"> <span class="p">}</span></span>
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2238
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<pre style="margin: 0;">+<span id="LC2238" class="line" lang="cpp"> <span class="p">}</span></span>
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2239
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<pre style="margin: 0;">+<span id="LC2239" class="line" lang="cpp"><span class="p">}</span></span>
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2240
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<pre style="margin: 0;">+<span id="LC2240" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2241
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<pre style="margin: 0;">+<span id="LC2241" class="line" lang="cpp"></span>
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2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VcfPhaseLookup4b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">cur_phased</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">);</span></span>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_phased_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">cur_phased</span><span class="p">);</span></span>
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2246
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<pre style="margin: 0;">+<span id="LC2246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phaseinfo_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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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2250
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<pre style="margin: 0;">+<span id="LC2250" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_phased_hw_shifted</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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2251
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<pre style="margin: 0;">+<span id="LC2251" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</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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2252
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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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2253
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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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2254
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<pre style="margin: 0;">+<span id="LC2254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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2255
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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2256
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<pre style="margin: 0;">+<span id="LC2256" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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2257
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<pre style="margin: 0;">+<span id="LC2257" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">]),</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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2258
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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="cpp"> <span class="p">}</span></span>
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2259
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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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2260
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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="cpp"> <span class="p">}</span></span>
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2261
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<pre style="margin: 0;">+<span id="LC2261" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2262
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<pre style="margin: 0;">+<span id="LC2262" class="line" lang="cpp"> <span class="p">}</span></span>
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2263
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<pre style="margin: 0;">+<span id="LC2263" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2264
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<pre style="margin: 0;">+<span id="LC2264" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_phased_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2265
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<pre style="margin: 0;">+<span id="LC2265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span><span class="p">)</span> <span class="p">{</span></span>
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2266
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<pre style="margin: 0;">+<span id="LC2266" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2267
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<pre style="margin: 0;">+<span id="LC2267" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">];</span></span>
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2268
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<pre style="margin: 0;">+<span id="LC2268" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2269
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<pre style="margin: 0;">+<span id="LC2269" class="line" lang="cpp"> <span class="p">}</span></span>
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2270
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<pre style="margin: 0;">+<span id="LC2270" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2271
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<pre style="margin: 0;">+<span id="LC2271" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2272
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<pre style="margin: 0;">+<span id="LC2272" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2273
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<pre style="margin: 0;">+<span id="LC2273" class="line" lang="cpp"></span>
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2274
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<pre style="margin: 0;">+<span id="LC2274" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// note that this must be on a separate line (or we have to static_cast)</span></span>
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2275
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<pre style="margin: 0;">+<span id="LC2275" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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2276
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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="cpp"></span>
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2277
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<pre style="margin: 0;">+<span id="LC2277" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2278
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<pre style="margin: 0;">+<span id="LC2278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">192</span><span class="p">);</span></span>
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2279
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<pre style="margin: 0;">+<span id="LC2279" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">];</span></span>
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2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2281
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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2283
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<pre style="margin: 0;">+<span id="LC2283" class="line" lang="cpp"> <span class="p">}</span></span>
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2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="cpp"> <span class="p">}</span></span>
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2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="cpp"> <span class="p">}</span></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="cpp"><span class="p">}</span></span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="cpp"></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVcfPhaseLookup4b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">)</span> <span class="p">{</span></span>
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2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="cpp"> <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;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">);</span></span>
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2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2293
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2295
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<pre style="margin: 0;">+<span id="LC2295" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2296
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2299" 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">
2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2300
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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2301
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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="cpp"> <span class="p">}</span></span>
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2306
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<pre style="margin: 0;">+<span id="LC2306" class="line" lang="cpp"> <span class="p">}</span></span>
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2307
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<pre style="margin: 0;">+<span id="LC2307" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [16][0]..[31][1]: first entry is phased and unflipped, second is unphased</span></span>
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2308
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<pre style="margin: 0;">+<span id="LC2308" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2309
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<pre style="margin: 0;">+<span id="LC2309" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2310
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<pre style="margin: 0;">+<span id="LC2310" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2311" 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">
2311
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<pre style="margin: 0;">+<span id="LC2311" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2312" 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">
2312
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<pre style="margin: 0;">+<span id="LC2312" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2313" 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">
2313
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<pre style="margin: 0;">+<span id="LC2313" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2314" 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">
2314
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<pre style="margin: 0;">+<span id="LC2314" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2315
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<pre style="margin: 0;">+<span id="LC2315" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2316" 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">
2316
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<pre style="margin: 0;">+<span id="LC2316" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2317" 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">
2317
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<pre style="margin: 0;">+<span id="LC2317" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2318" 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">
2318
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<pre style="margin: 0;">+<span id="LC2318" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2319
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<pre style="margin: 0;">+<span id="LC2319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2320
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<pre style="margin: 0;">+<span id="LC2320" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2321
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<pre style="margin: 0;">+<span id="LC2321" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2322
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<pre style="margin: 0;">+<span id="LC2322" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2323
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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="cpp"> <span class="p">}</span></span>
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2324
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<pre style="margin: 0;">+<span id="LC2324" class="line" lang="cpp"> <span class="p">}</span></span>
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2325
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<pre style="margin: 0;">+<span id="LC2325" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [32][0]..[63][1]: second entry is phased and unflipped</span></span>
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2326
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<pre style="margin: 0;">+<span id="LC2326" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2327
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<pre style="margin: 0;">+<span id="LC2327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2328
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<pre style="margin: 0;">+<span id="LC2328" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2329" 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">
2329
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<pre style="margin: 0;">+<span id="LC2329" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2330" 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">
2330
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<pre style="margin: 0;">+<span id="LC2330" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2331
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<pre style="margin: 0;">+<span id="LC2331" class="line" lang="cpp"> <span class="p">}</span></span>
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2332
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<pre style="margin: 0;">+<span id="LC2332" class="line" lang="cpp"> <span class="p">}</span></span>
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2333
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<pre style="margin: 0;">+<span id="LC2333" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2334
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<pre style="margin: 0;">+<span id="LC2334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2335" 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">
2335
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<pre style="margin: 0;">+<span id="LC2335" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2336" 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">
2336
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<pre style="margin: 0;">+<span id="LC2336" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2337" 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">
2337
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<pre style="margin: 0;">+<span id="LC2337" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2338" class="line" lang="cpp"> <span class="p">}</span></span>
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2339
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<pre style="margin: 0;">+<span id="LC2339" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2340" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [64][0]..[79][1] should be impossible</span></span>
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2341
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<pre style="margin: 0;">+<span id="LC2341" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">]);</span></span>
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2342
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<pre style="margin: 0;">+<span id="LC2342" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [80][0]..[95][1]: first entry is phased and flipped, second is unphased</span></span>
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2343
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<pre style="margin: 0;">+<span id="LC2343" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// genotype must be 01</span></span>
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2344
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<pre style="margin: 0;">+<span id="LC2344" class="line" lang="cpp"> <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;">phased_flipped_01</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2345
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<pre style="margin: 0;">+<span id="LC2345" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2346
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<pre style="margin: 0;">+<span id="LC2346" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2347
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2348
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<pre style="margin: 0;">+<span id="LC2348" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2349
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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="cpp"> <span class="p">}</span></span>
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2350
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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [96][0]..[111][1] should be impossible</span></span>
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2351
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">]);</span></span>
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2352
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<pre style="margin: 0;">+<span id="LC2352" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [112][0]..[127][1]: first entry phased-flipped, second phased-unflipped</span></span>
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2353
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<pre style="margin: 0;">+<span id="LC2353" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2354
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2355
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<pre style="margin: 0;">+<span id="LC2355" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2356
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [128][0]..[163][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2359" 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">
2359
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<pre style="margin: 0;">+<span id="LC2359" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">72</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2360" 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">
2360
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<pre style="margin: 0;">+<span id="LC2360" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [164][0]..[167][1]: second entry phased-flipped, first entry unphased</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2361" 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">
2361
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<pre style="margin: 0;">+<span id="LC2361" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2362" 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">
2362
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<pre style="margin: 0;">+<span id="LC2362" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2363" 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">
2363
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<pre style="margin: 0;">+<span id="LC2363" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2364
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<pre style="margin: 0;">+<span id="LC2364" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2365" 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">
2365
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<pre style="margin: 0;">+<span id="LC2365" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [168][0]..[179][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2366" 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">
2366
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<pre style="margin: 0;">+<span id="LC2366" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">24</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2367" 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">
2367
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<pre style="margin: 0;">+<span id="LC2367" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [180][0]..[183][1]: second entry phased-flipped, first phased-unflipped</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2368" 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">
2368
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<pre style="margin: 0;">+<span id="LC2368" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2369" 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">
2369
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<pre style="margin: 0;">+<span id="LC2369" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2370" 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">
2370
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<pre style="margin: 0;">+<span id="LC2370" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2371
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<pre style="margin: 0;">+<span id="LC2371" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2372" 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">
2372
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<pre style="margin: 0;">+<span id="LC2372" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [184][0]..[244][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2373" 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">
2373
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<pre style="margin: 0;">+<span id="LC2373" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [245][0]..[245][1]: both phased-flipped</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2374" 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">
2374
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<pre style="margin: 0;">+<span id="LC2374" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">122</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2375
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<pre style="margin: 0;">+<span id="LC2375" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">123</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2376
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<pre style="margin: 0;">+<span id="LC2376" class="line" lang="cpp"><span class="p">}</span></span>
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2377
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<pre style="margin: 0;">+<span id="LC2377" class="line" lang="cpp"></span>
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2378
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<pre style="margin: 0;">+<span id="LC2378" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VcfPhaseLookup2b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">cur_phased</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">);</span></span>
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2380
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<pre style="margin: 0;">+<span id="LC2380" class="line" lang="cpp"> <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;">sample_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_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;">kBitsPerWordD2</span><span class="p">;</span></span>
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2381
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<pre style="margin: 0;">+<span id="LC2381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_phased_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">cur_phased</span><span class="p">);</span></span>
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2382
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<pre style="margin: 0;">+<span id="LC2382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">phaseinfo_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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2383
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<pre style="margin: 0;">+<span id="LC2383" class="line" lang="cpp"> <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;">result_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2384" 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">
2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBitsPerWordD4</span><span class="p">;</span></span>
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2385
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<pre style="margin: 0;">+<span id="LC2385" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</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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2386
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<pre style="margin: 0;">+<span id="LC2386" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_phased_hw_shifted</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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2387
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<pre style="margin: 0;">+<span id="LC2387" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</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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2388
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<pre style="margin: 0;">+<span id="LC2388" class="line" lang="cpp"> <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;">widx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2389" 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">
2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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2391
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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2392
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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2393
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">result_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">]),</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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2394
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="cpp"> <span class="p">}</span></span>
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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="cpp"> <span class="p">}</span></span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModNz</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="cpp"> <span class="p">}</span></span>
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2399
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_phased_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span><span class="p">)</span> <span class="p">{</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">];</span></span>
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2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="cpp"> <span class="p">}</span></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="cpp"></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// note that this must be on a separate line (or we have to static_cast)</span></span>
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2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="cpp"></span>
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2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">loop_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">48</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">192</span><span class="p">);</span></span>
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2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_alias</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2416" 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">
2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_phased_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="cpp"> <span class="n" style="color: #333;">phaseinfo_hw_shifted</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="cpp"> <span class="p">}</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="cpp"> <span class="p">}</span></span>
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2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="cpp"> <span class="p">}</span></span>
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2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="cpp"><span class="p">}</span></span>
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2423
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<pre style="margin: 0;">+<span id="LC2423" class="line" lang="cpp"></span>
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2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVcfPhaseLookup2b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">)</span> <span class="p">{</span></span>
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2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">);</span></span>
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2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2427
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2428
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<pre style="margin: 0;">+<span id="LC2428" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2429" 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">
2429
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<pre style="margin: 0;">+<span id="LC2429" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2430" 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">
2430
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<pre style="margin: 0;">+<span id="LC2430" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2431" 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">
2431
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<pre style="margin: 0;">+<span id="LC2431" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2432" 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">
2432
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<pre style="margin: 0;">+<span id="LC2432" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2433" 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">
2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="cpp"> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2434" 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">
2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2435" 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">
2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2436
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<pre style="margin: 0;">+<span id="LC2436" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2437
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<pre style="margin: 0;">+<span id="LC2437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2438
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<pre style="margin: 0;">+<span id="LC2438" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2439" 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">
2439
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<pre style="margin: 0;">+<span id="LC2439" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2440
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<pre style="margin: 0;">+<span id="LC2440" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2441
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="cpp"> <span class="p">}</span></span>
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2442
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="cpp"> <span class="p">}</span></span>
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2443
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<pre style="margin: 0;">+<span id="LC2443" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [16][0]..[31][1]: first entry is phased and unflipped, second is unphased</span></span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2446
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</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;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2447
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</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;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2448
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<pre style="margin: 0;">+<span id="LC2448" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2449
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<pre style="margin: 0;">+<span id="LC2449" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2450
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<pre style="margin: 0;">+<span id="LC2450" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2451
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<pre style="margin: 0;">+<span id="LC2451" class="line" lang="cpp"> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">];</span></span>
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2452
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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2453
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<pre style="margin: 0;">+<span id="LC2453" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2454
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<pre style="margin: 0;">+<span id="LC2454" class="line" lang="cpp"> <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;">high_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2455
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<pre style="margin: 0;">+<span id="LC2455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2456
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<pre style="margin: 0;">+<span id="LC2456" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2457
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<pre style="margin: 0;">+<span id="LC2457" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2458
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<pre style="margin: 0;">+<span id="LC2458" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2459
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<pre style="margin: 0;">+<span id="LC2459" class="line" lang="cpp"> <span class="p">}</span></span>
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2460
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<pre style="margin: 0;">+<span id="LC2460" class="line" lang="cpp"> <span class="p">}</span></span>
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2461
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<pre style="margin: 0;">+<span id="LC2461" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [32][0]..[63][1]: second entry is phased and unflipped</span></span>
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2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2463
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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2464
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<pre style="margin: 0;">+<span id="LC2464" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2465
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<pre style="margin: 0;">+<span id="LC2465" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2467
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<pre style="margin: 0;">+<span id="LC2467" class="line" lang="cpp"> <span class="p">}</span></span>
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2468
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<pre style="margin: 0;">+<span id="LC2468" class="line" lang="cpp"> <span class="p">}</span></span>
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2469
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<pre style="margin: 0;">+<span id="LC2469" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2470
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<pre style="margin: 0;">+<span id="LC2470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2471
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<pre style="margin: 0;">+<span id="LC2471" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2472
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<pre style="margin: 0;">+<span id="LC2472" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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2473
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<pre style="margin: 0;">+<span id="LC2473" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_high</span><span class="p">;</span></span>
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2474
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<pre style="margin: 0;">+<span id="LC2474" class="line" lang="cpp"> <span class="p">}</span></span>
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2475
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<pre style="margin: 0;">+<span id="LC2475" class="line" lang="cpp"> <span class="p">}</span></span>
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2476
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<pre style="margin: 0;">+<span id="LC2476" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [64][0]..[79][1] should be impossible</span></span>
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2477
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<pre style="margin: 0;">+<span id="LC2477" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">]);</span></span>
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2478
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [80][0]..[95][1]: first entry is phased and flipped, second is unphased</span></span>
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2479
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<pre style="margin: 0;">+<span id="LC2479" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// genotype must be 01</span></span>
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2480
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="cpp"> <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;">phased_flipped_01</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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2481
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<pre style="margin: 0;">+<span id="LC2481" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2482
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<pre style="margin: 0;">+<span id="LC2482" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2483
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<pre style="margin: 0;">+<span id="LC2483" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2484
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<pre style="margin: 0;">+<span id="LC2484" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2485
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="cpp"> <span class="p">}</span></span>
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2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [96][0]..[111][1] should be impossible</span></span>
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2487
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<pre style="margin: 0;">+<span id="LC2487" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">32</span><span class="p">]);</span></span>
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2488
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<pre style="margin: 0;">+<span id="LC2488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [112][0]..[127][1]: first entry phased-flipped, second phased-unflipped</span></span>
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2489
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<pre style="margin: 0;">+<span id="LC2489" class="line" lang="cpp"> <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;">high_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;">high_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">high_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2490
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2491
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<pre style="margin: 0;">+<span id="LC2491" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">high_idx</span><span class="p">];</span></span>
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2492
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<pre style="margin: 0;">+<span id="LC2492" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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2493
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<pre style="margin: 0;">+<span id="LC2493" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2494" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [128][0]..[163][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2495" 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">
2495
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<pre style="margin: 0;">+<span id="LC2495" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">72</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2496" 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">
2496
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<pre style="margin: 0;">+<span id="LC2496" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [164][0]..[167][1]: second entry phased-flipped, first entry unphased</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2497" 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">
2497
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<pre style="margin: 0;">+<span id="LC2497" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2498" 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">
2498
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<pre style="margin: 0;">+<span id="LC2498" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unphased_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2499" 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">
2499
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<pre style="margin: 0;">+<span id="LC2499" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2500
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<pre style="margin: 0;">+<span id="LC2500" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2501" 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">
2501
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<pre style="margin: 0;">+<span id="LC2501" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [168][0]..[179][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2502" 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">
2502
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<pre style="margin: 0;">+<span id="LC2502" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">24</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2503" 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">
2503
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<pre style="margin: 0;">+<span id="LC2503" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [180][0]..[183][1]: second entry phased-flipped, first phased-unflipped</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2504" 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">
2504
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<pre style="margin: 0;">+<span id="LC2504" class="line" lang="cpp"> <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;">low_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;">low_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">low_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2505" 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">
2505
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<pre style="margin: 0;">+<span id="LC2505" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_unflipped_vals</span><span class="p">[</span><span class="n" style="color: #333;">low_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2506" 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">
2506
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<pre style="margin: 0;">+<span id="LC2506" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">table_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2507" 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">
2507
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<pre style="margin: 0;">+<span id="LC2507" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2508" 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">
2508
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<pre style="margin: 0;">+<span id="LC2508" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [184][0]..[244][1] should be impossible</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2509" 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">
2509
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<pre style="margin: 0;">+<span id="LC2509" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [245][0]..[245][1]: both phased-flipped</span></span>
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<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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<pre style="margin: 0;">+<span id="LC2510" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">122</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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<td class="diff-line-num new new_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">
2511
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<pre style="margin: 0;">+<span id="LC2511" class="line" lang="cpp"> <span class="n" style="color: #333;">table_iter</span><span class="p">[</span><span class="mi" style="color: #099;">123</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phased_flipped_01</span><span class="p">;</span></span>
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2512
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<pre style="margin: 0;">+<span id="LC2512" class="line" lang="cpp"><span class="p">}</span></span>
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2513
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<pre style="margin: 0;">+<span id="LC2513" class="line" lang="cpp"></span>
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2514
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<pre style="margin: 0;">+<span id="LC2514" class="line" lang="cpp"></span>
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1928
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<td class="diff-line-num new_line" data-linenumber="2515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2515
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<pre style="margin: 0;"> <span id="LC2515" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ClearGenoarrMissing1bit8Unsafe</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">genoarr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subset_sizep</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">subset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">sparse_vals</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2516" class="line" lang="cpp"> <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;">orig_subset_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">subset_sizep</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2517" class="line" lang="cpp"> <span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">subset_alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">Halfword</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">subset</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#e77f6102ff6675b5bc8947f913bdad39d3e254f4"><strong>include/pgenlib_misc.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,7 +79,7 @@</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 10000 * major + 100 * minor + patch</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Exception to CONSTI32, since we want the preprocessor to have access to this</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// value. Named with all caps as a consequence.</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PGENLIB_INTERNAL_VERNUM 150<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PGENLIB_INTERNAL_VERNUM 150<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">plink2</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -472,6 +472,8 @@ void SplitHomRef2het(const uintptr_t* genoarr, uint32_t sample_ct, uintptr_t* __</td>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// so they aren't always the right choice.</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// When lookup table rows are 16 bytes, they are assumed to be 16-byte aligned</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// in 64-bit builds. result[] is not assumed to be aligned.</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrLookup256x1bx4</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrLookup16x4bx2</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table16x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrLookup256x2bx4</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x2bx4</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -515,6 +517,10 @@ void InitLookup16x4bx2(void* table16x4bx2);</td>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup16x8bx2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table16x8bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x1bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x1bx4</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x2bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x2bx4</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitLookup256x4bx4</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table256x4bx4</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PhaseLookup4b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phasepresent</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -522,6 +528,10 @@ void PhaseLookup4b(const uintptr_t* genoarr, const uintptr_t* phasepresent, cons</td>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// [0][0]..[3][0], [17][0], and [19][0] should contain the relevant values</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitPhaseLookup4b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x4bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PhaseLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phasepresent</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitPhaseLookup8b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table56x8bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// het-haploid prohibited. 64-entry table suffices: we use the same bits for</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// phasepresent and sex_male since they can't be true simultaneously.</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// phaseinfo is xor'd with bits 1 and 3 instead of 1 and 2.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -533,6 +543,25 @@ void InitPhaseXNohhLookup4b(void* table64x4bx2);</td>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uses same table as PhaseXNohhLookup</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrSexLookup4b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitPhaseXNohhLookup8b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrSexLookup8b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table64x8bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Unlike PhaseLookup4b(), this allows the cur_phased bit to be set when the</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// genoarr entry is not 01 (het).</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VcfPhaseLookup4b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">cur_phased</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Precondition:</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// [0], [2], [4], [6] initialized with unphased entries</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// [32], [34], [36], [38] initialized with phased-unflipped entries</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// [162] initialized with phased-flipped case</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVcfPhaseLookup4b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x4bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VcfPhaseLookup2b</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">cur_phased</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">phaseinfo</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVcfPhaseLookup2b</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">table246x2bx2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Analogue of BitIter1x.</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GenoIter1x</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">genoarr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">match_word</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">widxp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">cur_bitsp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_bitsp</span><span class="p">;</span></span>
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<li id="4776c94d0e4a55582487ac9c960d27e25dcb2101">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#4776c94d0e4a55582487ac9c960d27e25dcb2101"><strong>include/pgenlib_read.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6636,39 +6636,39 @@ PglErr ParseAux2Subset(const unsigned char* fread_end, const uintptr_t* __restri</td>
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<pre style="margin: 0;"> <span id="LC6636" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC6637" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpandThenSubsetBytearr</span><span class="p">(</span><span class="n" style="color: #333;">aux2_start</span><span class="p">,</span> <span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">het_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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6638
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<pre style="margin: 0;"> <span id="LC6638" class="line" lang="cpp"> <span class="p">}</span></span>
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6639
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<pre style="margin: 0;">-<span id="LC6639" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">phasepresent_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC6640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6641" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC6642" class="line" lang="cpp"> <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;">het_ctdl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kBitsPerWord</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6639" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (25 Feb 2020): forgot to mask out subsetted_10het here</span></span>
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<pre style="margin: 0;">+<span id="LC6640" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6641" class="line" lang="cpp"> <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;">het_ctdl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kBitsPerWord</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6642" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC6644" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// explicit phasepresent</span></span>
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<pre style="margin: 0;">-<span id="LC6645" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <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;">aux2_first_part</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_start</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC6646" class="line" lang="cpp"> <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;">aux2_first_part_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">workspace_subset</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6647" class="line" lang="cpp"> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">[</span><span class="n" style="color: #333;">het_ctdl</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>
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<pre style="margin: 0;">-<span id="LC6648" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">));</span></span>
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6649
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<pre style="margin: 0;">-<span id="LC6649" class="line" lang="cpp"> <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;">raw_phasepresent_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">het_ctdl</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6650
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<pre style="margin: 0;">-<span id="LC6650" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">))</span> <span class="p">{</span></span>
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6651
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<pre style="margin: 0;">-<span id="LC6651" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there shouldn't be a hphase track at all in this case</span></span>
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<pre style="margin: 0;">-<span id="LC6652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6653" class="line" lang="cpp"> <span class="p">}</span></span>
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6654
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<pre style="margin: 0;">-<span id="LC6654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aux2_second_part</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">aux2_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">)]);</span></span>
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<pre style="margin: 0;">-<span id="LC6655" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fread_pp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aux2_second_part</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PtrAddCk</span><span class="p">(</span><span class="n" style="color: #333;">fread_end</span><span class="p">,</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">),</span> <span class="n" style="color: #333;">fread_pp</span><span class="p">))</span> <span class="p">{</span></span>
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6657
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<pre style="margin: 0;">-<span id="LC6657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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6658
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<pre style="margin: 0;">-<span id="LC6658" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC6659" class="line" lang="cpp"> <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;">phaseinfo</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC6660" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6661" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC6662" class="line" lang="cpp"> <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;">sample_include</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC6663" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpandBytearrNested</span><span class="p">(</span><span class="n" style="color: #333;">aux2_second_part</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC6664" class="line" lang="cpp"> <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;">subsetted_10het</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC6665" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">phasepresent_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6643" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// explicit phasepresent</span></span>
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6644
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<pre style="margin: 0;">+<span id="LC6644" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <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;">aux2_first_part</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_start</span><span class="p">);</span></span>
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6645
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<pre style="margin: 0;">+<span id="LC6645" class="line" lang="cpp"> <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;">aux2_first_part_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">workspace_subset</span><span class="p">;</span></span>
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6646
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<pre style="margin: 0;">+<span id="LC6646" class="line" lang="cpp"> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">[</span><span class="n" style="color: #333;">het_ctdl</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>
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6647
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<pre style="margin: 0;">+<span id="LC6647" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">));</span></span>
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6648
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<pre style="margin: 0;">+<span id="LC6648" class="line" lang="cpp"> <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;">raw_phasepresent_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">het_ctdl</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6649
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<pre style="margin: 0;">+<span id="LC6649" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">))</span> <span class="p">{</span></span>
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6650
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<pre style="margin: 0;">+<span id="LC6650" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there shouldn't be a hphase track at all in this case</span></span>
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6651
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<pre style="margin: 0;">+<span id="LC6651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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6652
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<pre style="margin: 0;">+<span id="LC6652" class="line" lang="cpp"> <span class="p">}</span></span>
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6653
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<pre style="margin: 0;">+<span id="LC6653" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aux2_second_part</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">aux2_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">het_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">)]);</span></span>
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6654
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<pre style="margin: 0;">+<span id="LC6654" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fread_pp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aux2_second_part</span><span class="p">;</span></span>
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6655
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<pre style="margin: 0;">+<span id="LC6655" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PtrAddCk</span><span class="p">(</span><span class="n" style="color: #333;">fread_end</span><span class="p">,</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">),</span> <span class="n" style="color: #333;">fread_pp</span><span class="p">))</span> <span class="p">{</span></span>
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6656
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<pre style="margin: 0;">+<span id="LC6656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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6657
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<pre style="margin: 0;">+<span id="LC6657" class="line" lang="cpp"> <span class="p">}</span></span>
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6658
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<pre style="margin: 0;">+<span id="LC6658" class="line" lang="cpp"> <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;">phaseinfo</span><span class="p">)</span> <span class="p">{</span></span>
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6666
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6659
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<pre style="margin: 0;"> <span id="LC6659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6660" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC6668" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC6669" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// could skip if intersection of phasepresent with sample_include is empty,</span></span>
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<pre style="margin: 0;">-<span id="LC6670" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// but this function call should be fast enough there anyway?</span></span>
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<pre style="margin: 0;">-<span id="LC6671" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpandThenSubsetBytearrNested</span><span class="p">(</span><span class="n" style="color: #333;">aux2_second_part</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC6661" class="line" lang="cpp"> <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;">sample_include</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6662" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpandBytearrNested</span><span class="p">(</span><span class="n" style="color: #333;">aux2_second_part</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC6663" class="line" lang="cpp"> <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;">subsetted_10het</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6664" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">phasepresent_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6666" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6667" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6668" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// could skip if intersection of phasepresent with sample_include is</span></span>
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<pre style="margin: 0;">+<span id="LC6669" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// empty, but this function call should be fast enough there anyway?</span></span>
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<pre style="margin: 0;">+<span id="LC6670" class="line" lang="cpp"> <span class="n" style="color: #333;">ExpandThenSubsetBytearrNested</span><span class="p">(</span><span class="n" style="color: #333;">aux2_second_part</span><span class="p">,</span> <span class="n" style="color: #333;">aux2_first_part_copy</span><span class="p">,</span> <span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">raw_phasepresent_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC6671" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC6672" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC6673" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subsetted_10het</span><span class="p">)</span> <span class="p">{</span></span>
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6674
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<pre style="margin: 0;"> <span id="LC6674" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmask</span><span class="p">(</span><span class="n" style="color: #333;">subsetted_10het</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">phasepresent</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#5fce52c5aa6c7bce70dfbc7bf69033d4e1b69e50"><strong>include/plink2_base.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,11 +173,11 @@ BoolErr ScanIntAbsBounded(const char* str_iter, uint64_t bound, int32_t* valp) {</td>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <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;">valp</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">sign</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>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <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 class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">valp</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">5</span></span><span class="p">)</span> <span class="p">{</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">unlikely</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">valp</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">5</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">ctou32</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">valp</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span> <span class="p">{</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">valp</span></span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span> <span class="p">{</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="p">}</span></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="260" style="width: 35px; color: rgba(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="260" style="width: 35px; color: rgba(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">@@ -260,7 +260,7 @@ BoolErr ScanIntAbsBounded32(const char* str_iter, uint32_t bound_div_10, uint32_</td>
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260
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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261
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0xfffffffdU</span><span class="p">)</span> <span class="p">{</span></span>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">sign</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>
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263
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<td class="diff-line-num new_line old" data-linenumber="263" 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="LC263" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">val</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mh" style="color: #099;"><span class="idiff right">0xfffffffbU</span></span><span class="p">)</span> <span class="p">{</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">unlikely</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mh" style="color: #099;"><span class="idiff">0xfffffffbU</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="p">}</span></span>
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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#f2695700d4614304f2acf05f9546dcf4b3608c47"><strong>include/plink2_base.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1019" style="width: 35px; color: rgba(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="1019" style="width: 35px; color: rgba(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">@@ -1019,6 +1019,10 @@ HEADER_INLINE void vecw_storeu(void* mem_addr, VecW vv) {</td>
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1019
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_si256</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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1020
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1021
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<td class="diff-line-num new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1022" 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="1022" 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">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">vecu32_storeu</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1023" 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">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_si256</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" 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">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1025" 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">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"></span>
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1022
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<td class="diff-line-num new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">veci32_storeu</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">,</span> <span class="n" style="color: #333;">VecI32</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm256_storeu_si256</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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1024
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<td class="diff-line-num new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1059" style="width: 35px; color: rgba(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="1063" style="width: 35px; color: rgba(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">@@ -1059,6 +1063,18 @@ HEADER_INLINE VecUc vecuc_min(VecUc v1, VecUc v2) {</td>
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1059
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<td class="diff-line-num new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecUc</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_min_epu8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">v1</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">)));</span></span>
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1060
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<td class="diff-line-num new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<td class="diff-line-num new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1062" 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="1066" 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">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vecw_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1062" 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="1067" 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">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"><span class="p">}</span></span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">vecu32_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1071" 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">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecU32</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"><span class="p">}</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vecu16_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecU16</span><span class="p">,</span> <span class="n" style="color: #333;">_mm256_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m256i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"><span class="p">}</span></span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp"></span>
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1062
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1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else // !USE_AVX2</span></span>
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1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="cpp"></span>
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1064
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># define VCONST_W(xx) {xx, xx}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1238" style="width: 35px; color: rgba(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="1254" style="width: 35px; color: rgba(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">@@ -1238,6 +1254,10 @@ HEADER_INLINE void vecw_storeu(void* mem_addr, VecW vv) {</td>
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1254
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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1239
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="cpp"><span class="p">}</span></span>
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1240
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1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="cpp"></span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">vecu32_storeu</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1258" 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">
1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"><span class="p">}</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"></span>
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1241
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1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">veci32_storeu</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">,</span> <span class="n" style="color: #333;">VecI32</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1242
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<td class="diff-line-num new_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"> <span class="n" style="color: #333;">_mm_storeu_si128</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">mem_addr</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">));</span></span>
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1243
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<td class="diff-line-num new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1368" style="width: 35px; color: rgba(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="1388" style="width: 35px; color: rgba(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">@@ -1368,6 +1388,18 @@ HEADER_INLINE uintptr_t vecw_extract64_0(VecW vv) {</td>
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1368
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1388
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">vecw_extract64_1</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<td class="diff-line-num new_line" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1389
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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_mm_extract_epi64</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1370
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<td class="diff-line-num new_line" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1371" 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="1391" 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">
1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1371" 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="1392" 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">
1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vecw_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1371" 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="1393" 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">
1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1394" 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">
1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1371" 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="1395" 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">
1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1371" 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="1396" 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">
1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">vecu32_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1397" 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">
1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecU32</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1398" 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">
1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1399" 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">
1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1400" 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">
1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vecu16_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1401" 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">
1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecU16</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_blendv_epi8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">bb</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">)));</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="cpp"><span class="p">}</span></span>
</pre>
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1371
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1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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1372
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1404
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">vecw_extract64_0</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="p">{</span></span>
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1373
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_movepi64_pi64</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">)));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1377" style="width: 35px; color: rgba(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="1409" style="width: 35px; color: rgba(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">@@ -1377,6 +1409,20 @@ HEADER_INLINE uintptr_t vecw_extract64_1(VecW vv) {</td>
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1377
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">v0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_srli_si128</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">vv</span><span class="p">),</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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1378
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_movepi64_pi64</span><span class="p">(</span><span class="n" style="color: #333;">v0</span><span class="p">));</span></span>
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1379
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1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp"><span class="p">}</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1413" 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">
1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// N.B. we do *not* enforce the low bits of each mask byte matching the high</span></span>
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1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bit.</span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vecw_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vecw_and_notfirst</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bb</span><span class="p">);</span></span>
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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"><span class="p">}</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="cpp"></span>
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1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">vecu32_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU32</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1420" 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">
1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vecu32_and_notfirst</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bb</span><span class="p">);</span></span>
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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="cpp"><span class="p">}</span></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1423" 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">
1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vecu16_blendv</span><span class="p">(</span><span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">aa</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">bb</span><span class="p">,</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1424" 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">
1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">vecu16_and_notfirst</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">aa</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bb</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="cpp"><span class="p">}</span></span>
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1380
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1426
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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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1381
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1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="cpp"></span>
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1382
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1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecI16</span> <span class="n" style="color: #333;">veci16_max</span><span class="p">(</span><span class="n" style="color: #333;">VecI16</span> <span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">VecI16</span> <span class="n" style="color: #333;">v2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1398" style="width: 35px; color: rgba(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="1444" style="width: 35px; color: rgba(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">@@ -1398,7 +1444,6 @@ HEADER_INLINE VecU16 vecu16_min8(VecU16 v1, VecU16 v2) {</td>
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1398
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecUc</span> <span class="n" style="color: #333;">vecuc_min</span><span class="p">(</span><span class="n" style="color: #333;">VecUc</span> <span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">VecUc</span> <span class="n" style="color: #333;">v2</span><span class="p">)</span> <span class="p">{</span></span>
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1399
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecUc</span><span class="p">,</span> <span class="n" style="color: #333;">_mm_min_epu8</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">v1</span><span class="p">),</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">)));</span></span>
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1400
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="cpp"><span class="p">}</span></span>
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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="cpp"></span>
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1402
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1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif // !USE_AVX2</span></span>
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1403
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1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="cpp"></span>
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1404
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">vecw_bytesum</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">m0</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#df87a656e39e60d062ab0047bd78b5260a146504"><strong>include/plink2_bits.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1682" style="width: 35px; color: rgba(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">@@ -1682,12 +1682,12 @@ void TransposeBitblock64(const uintptr_t* read_iter, uintptr_t read_ul_stride, u</td>
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1682
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1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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1683
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1683
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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">loader0</span><span class="p">,</span> <span class="n" style="color: #333;">loader1</span><span class="p">);</span></span>
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1684
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<pre style="margin: 0;"> <span id="LC1684" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">loader0</span><span class="p">,</span> <span class="n" style="color: #333;">loader1</span><span class="p">);</span></span>
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1685
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<pre style="margin: 0;">-<span id="LC1685" class="line" lang="cpp"> <span class="n" style="color: #333;">loader0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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1686
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC1686" class="line" lang="cpp"> <span class="n" style="color: #333;">loader1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="cpp"> <span class="n" style="color: #333;">loader0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="cpp"> <span class="n" style="color: #333;">loader1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">loader2</span><span class="p">,</span> <span class="n" style="color: #333;">loader3</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1688" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">loader2</span><span class="p">,</span> <span class="n" style="color: #333;">loader3</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1689" class="line" lang="cpp"> <span class="n" style="color: #333;">loader2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC1690" class="line" lang="cpp"> <span class="n" style="color: #333;">loader3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="cpp"> <span class="n" style="color: #333;">loader2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="cpp"> <span class="n" style="color: #333;">loader3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -> (0,0) (1,0) (2,0) (3,0) (0,1) (1,1) (2,1) (3,1) (0,2) ...</span></span>
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<pre style="margin: 0;"> <span id="LC1693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">lo_0123</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo16</span><span class="p">(</span><span class="n" style="color: #333;">loader0</span><span class="p">,</span> <span class="n" style="color: #333;">loader1</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2086,20 +2086,20 @@ void TransposeNybbleblock(const uintptr_t* read_iter, uint32_t read_ul_stride, u</td>
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<pre style="margin: 0;"> <span id="LC2086" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else</span></span>
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<pre style="margin: 0;"> <span id="LC2087" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles0</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2088" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles0</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC2090" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles1</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles1</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2093" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles2</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles2</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2097" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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2099
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<pre style="margin: 0;"> <span id="LC2099" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles3</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles3</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpackhi8</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles3</span><span class="p">,</span> <span class="n" style="color: #333;">odd_nybbles3</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">-<span id="LC2102" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</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">m8</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">vecw_and_notfirst</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m8</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">tmp_hi</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2101" class="line" lang="cpp"> <span class="n" style="color: #333;">even_nybbles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vecw_slli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="cpp"> <span class="n" style="color: #333;">odd_nybbles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">vecw_blendv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_hi</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vecw_srli</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_lo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">8</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">m8</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2103" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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<pre style="margin: 0;"> <span id="LC2104" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC2105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span> <span class="n" style="color: #333;">even_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecw_unpacklo16</span><span class="p">(</span><span class="n" style="color: #333;">even_nybbles0</span><span class="p">,</span> <span class="n" style="color: #333;">even_nybbles1</span><span class="p">);</span></span>
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<li id="b294a1a5c458bca5a817f674d97272b064975c1a">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#b294a1a5c458bca5a817f674d97272b064975c1a"><strong>include/plink2_bits.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -504,6 +504,8 @@ uintptr_t CountByte(const void* bytearr, unsigned char ucc, uintptr_t byte_ct);</td>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">CountU16</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">u16arr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">usii</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">u16_ct</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Applies sample_include to {src_subset, src_vals}.</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Copy1bit8Subset</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">src_vals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">src_subset_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">dst_vals</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Copy1bit16Subset</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">src_vals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">src_subset_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">dst_vals</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#4b320ace526dc39d7e8f303b1481e411020379dc"><strong>include/plink2_string.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1047,6 +1047,31 @@ BoolErr ScanmovUintCapped(uint64_t cap, const char** str_iterp, uint32_t* valp)</td>
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1047
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_iter</span><span class="p">;</span></span>
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScanmovUintCappedFinish</span><span class="p">(</span><span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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1049
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp"><span class="p">}</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 2^{-31} < floor <= 0 <= cap < 2^31</span></span>
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovIntBounded</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">abs_floor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sign</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"> <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;">valp</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">sign</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>
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs_floor</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"> <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;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// accept leading '+'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" 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">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1065" 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">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1066" 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">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1067" 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">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" 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">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ScanmovUintCappedFinish</span><span class="p">(</span><span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">valp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" 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">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1072" 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">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sign</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1073" 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">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"><span class="p">}</span></span>
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1050
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1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1051
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<td class="diff-line-num new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovPosintCapped32</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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1052
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<td class="diff-line-num new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1077
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1111" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1111,6 +1136,37 @@ BoolErr ScanmovUintCapped32(uint32_t cap_div_10, uint32_t cap_mod_10, const char</td>
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1111
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cur_digit</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1112
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<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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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"> <span class="p">}</span></span>
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1113
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1138
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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp"><span class="p">}</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovIntBounded32</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">abs_floor_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">abs_floor_mod_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1142" 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">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1143" 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">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sign</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1144" 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">
1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1145" 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">
1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0xfffffffdU</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1146" 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">
1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="n" style="color: #333;">sign</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>
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<td class="diff-line-num new new_line" data-linenumber="1147" 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">
1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="n" style="color: #333;">cap_div_10</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs_floor_div_10</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1148" 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">
1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="n" style="color: #333;">cap_mod_10</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs_floor_mod_10</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1149" 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">
1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp"> <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;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mh" style="color: #099;">0xfffffffbU</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1150" 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">
1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="cpp"> <span class="p">}</span></span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">))</span> <span class="p">{</span></span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp"> <span class="p">}</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="cpp"> <span class="p">}</span></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">str_iter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_digit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">48</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1159" 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">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_digit</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1160" 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">
1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">valp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sign</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">S_CAST</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;">val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1161" 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">
1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_iterp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1162" 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">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="p">}</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cur_digit</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1165" 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">
1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="cpp"> <span class="p">}</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cur_digit</span><span class="p">;</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="cpp"> <span class="p">}</span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="cpp"><span class="p">}</span></span>
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1114
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1115
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="cpp"></span>
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1116
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="cpp"><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;">double</span> <span class="n" style="color: #333;">kPositivePow10</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e1</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e3</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e4</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e5</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e6</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e7</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e8</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e9</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e10</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e11</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e12</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e13</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e14</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0e15</span><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3091" style="width: 35px; color: rgba(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="3147" style="width: 35px; color: rgba(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">@@ -3091,6 +3147,30 @@ uintptr_t ExpsearchNsortStrLb(const char* idbuf, const char* nsorted_strbox, uin</td>
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3091
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3147
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<pre style="margin: 0;"> <span id="LC3147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">start_idx</span><span class="p">;</span></span>
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3092
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3148
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<pre style="margin: 0;"> <span id="LC3148" class="line" lang="cpp"><span class="p">}</span></span>
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3093
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3149
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<pre style="margin: 0;"> <span id="LC3149" class="line" lang="cpp"></span>
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3150
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<pre style="margin: 0;">+<span id="LC3150" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IsInfStr</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">is_neg_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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3151
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<pre style="margin: 0;">+<span id="LC3151" class="line" lang="cpp"> <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;">first_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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3152
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<pre style="margin: 0;">+<span id="LC3152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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3153
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<pre style="margin: 0;">+<span id="LC3153" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">is_neg_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3154
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<pre style="margin: 0;">+<span id="LC3154" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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3155
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<pre style="margin: 0;">+<span id="LC3155" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">slen</span><span class="p">;</span></span>
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3156
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<pre style="margin: 0;">+<span id="LC3156" class="line" lang="cpp"> <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;">first_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span><span class="p">)</span> <span class="p">{</span></span>
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3157
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<pre style="margin: 0;">+<span id="LC3157" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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3158
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<pre style="margin: 0;">+<span id="LC3158" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">slen</span><span class="p">;</span></span>
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3159
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<pre style="margin: 0;">+<span id="LC3159" class="line" lang="cpp"> <span class="p">}</span></span>
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3160
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<pre style="margin: 0;">+<span id="LC3160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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3161
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<pre style="margin: 0;">+<span id="LC3161" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">four_chars</span><span class="p">;</span></span>
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3162
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<pre style="margin: 0;">+<span id="LC3162" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">four_chars</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// OVERREAD</span></span>
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3163
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<pre style="margin: 0;">+<span id="LC3163" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assumes little-endian</span></span>
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3164
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<pre style="margin: 0;">+<span id="LC3164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="n" style="color: #333;">four_chars</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xdfdfdf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x464e49</span><span class="p">);</span></span>
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3165
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<pre style="margin: 0;">+<span id="LC3165" class="line" lang="cpp"> <span class="p">}</span></span>
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3166
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<pre style="margin: 0;">+<span id="LC3166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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3167
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<pre style="margin: 0;">+<span id="LC3167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3168
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<pre style="margin: 0;">+<span id="LC3168" class="line" lang="cpp"> <span class="p">}</span></span>
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3169
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<pre style="margin: 0;">+<span id="LC3169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">eight_chars</span><span class="p">;</span></span>
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3170
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<pre style="margin: 0;">+<span id="LC3170" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">eight_chars</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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3171
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<pre style="margin: 0;">+<span id="LC3171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="n" style="color: #333;">eight_chars</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xdfdfdfdfdfdfdfdfLLU</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x5954494e49464e49LLU</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3172" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3173" class="line" lang="cpp"></span>
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3174
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<pre style="margin: 0;"> <span id="LC3174" class="line" lang="cpp"></span>
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3175
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<pre style="margin: 0;"> <span id="LC3175" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LP64__</span></span>
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3096
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3176
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<pre style="margin: 0;"> <span id="LC3176" class="line" lang="cpp"><span class="n" style="color: #333;">CXXCONST_CP</span> <span class="n" style="color: #333;">Memrchr</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">needle</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">slen</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#e04ad6b4524c358c1efeb53be9496b769cc2fe19"><strong>include/plink2_string.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -921,11 +921,16 @@ BoolErr ScanPosintptr(const char* str_iter, uintptr_t* valp);</td>
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovPosintCapped</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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922
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922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"></span>
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923
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923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovUintCapped</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 2^{-31} < -abs_floor <= 0 <= cap < 2^31</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" 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">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovIntBounded</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">abs_floor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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924
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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925
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovPosintCapped32</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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926
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"></span>
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927
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovUintCapped32</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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928
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp"></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovIntBounded32</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">abs_floor_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">abs_floor_mod_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_div_10</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap_mod_10</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"></span>
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929
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovPosintCapped</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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930
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScanmovPosintCapped32</span><span class="p">(</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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931
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="933" style="width: 35px; color: rgba(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="938" style="width: 35px; color: rgba(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">@@ -933,6 +938,10 @@ HEADER_INLINE BoolErr ScanmovPosintCapped(uint32_t cap, const char** str_iterp,</td>
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933
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovUintCapped</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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934
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<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
939
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<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScanmovUintCapped32</span><span class="p">(</span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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935
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="941" 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">
941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="942" 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">
942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovIntBounded</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">abs_floor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="943" 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">
943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ScanmovIntBounded32</span><span class="p">(</span><span class="n" style="color: #333;">abs_floor</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">abs_floor</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="n" style="color: #333;">valp</span><span class="p">);</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"><span class="p">}</span></span>
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936
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945
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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937
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="cpp"></span>
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938
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ScanmovUintDefcap</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">str_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">valp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1524" style="width: 35px; color: rgba(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="1533" style="width: 35px; color: rgba(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">@@ -1524,6 +1533,11 @@ HEADER_INLINE uint32_t IsNanStr(const char* ss, uint32_t slen) {</td>
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1524
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1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">ctou32</span><span class="p">(</span><span class="n" style="color: #333;">ss</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xdf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">78</span><span class="p">);</span></span>
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1525
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="cpp"><span class="p">}</span></span>
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1526
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1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="cpp"></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Matches "inf"/"infinity", any capitalization, can have sign in front.</span></span>
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assumes is_neg zero-initialized.</span></span>
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assumes one-char overread is ok.</span></span>
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1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IsInfStr</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">is_neg_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="cpp"></span>
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">CXXCONST_CP</span> <span class="n" style="color: #333;">AdvToDelimOrEnd</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_iter</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delim</span><span class="p">)</span> <span class="p">{</span></span>
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="cpp"> <span class="n" style="color: #333;">CXXCONST_CP</span> <span class="n" style="color: #333;">memchr_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">CXXCONST_CP</span><span class="p">,</span> <span class="n" style="color: #333;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">str_iter</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">str_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">str_iter</span><span class="p">));</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#21867eb3deeaf9db3872b9470e5dd6366a2591cf"><strong>pgenlibr/src/Makevars</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">SOURCES = $(wildcard libdeflate/lib/*.c) $(wildcard libdeflate/lib/x86/*.c)</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">OBJECTS = include/plink2_base.o include/pgenlib_misc.o include/pgenlib_read.o pvar_ffi_support.o pgenlib_ffi_support.o include/plink2_bgzf.o include/plink2_string.o include/plink2_text.o include/plink2_thread.o include/plink2_zstfile.o pvar.o pgenlibr.o RcppExports.o $(SOURCES:.c=.o)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">OBJECTS = include/plink2_base.o include/p<span class="idiff left right">link2_bits.o include/p</span>genlib_misc.o include/pgenlib_read.o pvar_ffi_support.o pgenlib_ffi_support.o include/plink2_bgzf.o include/plink2_string.o include/plink2_text.o include/plink2_thread.o include/plink2_zstfile.o pvar.o pgenlibr.o RcppExports.o $(SOURCES:.c=.o)</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">PKG_CFLAGS = -Ilibdeflate -Ilibdeflate/common</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">PKG_CPPFLAGS =</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">PKG_LIBS = -lpthread -lzstd</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f"><strong>plink2.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +66,7 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_MKL</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Intel"</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (<span class="idiff left right">17 Feb</span> 2020)"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (<span class="idiff left right">21 Mar</span> 2020)"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2523" style="width: 35px; color: rgba(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="2523" style="width: 35px; color: rgba(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">@@ -2523,12 +2523,12 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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2523
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2523
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<pre style="margin: 0;"> <span id="LC2523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">command_flags1</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfCommand1MakePlink2</span><span class="p">)</span> <span class="p">{</span></span>
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2524
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2524
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<pre style="margin: 0;"> <span id="LC2524" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// todo: unsorted case (--update-chr, etc.)</span></span>
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2525
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2525
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<pre style="margin: 0;"> <span id="LC2525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sort_vars_flags</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kfSort0</span><span class="p">)</span> <span class="p">{</span></span>
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2526
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<pre style="margin: 0;">-<span id="LC2526" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_include</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="n" style="color: #333;"><span class="idiff">pii</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></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">pvarname</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><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">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sort_vars_flags</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">kfSortNatural</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">pvar_psam_flags</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2526" 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">
2526
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<pre style="margin: 0;">+<span id="LC2526" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sample_include</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="n" style="color: #333;"><span class="idiff">pii</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></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">pvarname</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><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">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sort_vars_flags</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">kfSortNatural</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">xheader</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2527" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vpos_sortstatus</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfUnsortedVarBp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2529" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Variants are not sorted by position. Consider rerunning with the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">--sort-vars flag added to remedy this.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2530" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC2531" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_include</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="n" style="color: #333;"><span class="idiff">pii</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></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">pvarname</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pgr_alloc_cacheline_ct</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgfi</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2531" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">sample_include</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="n" style="color: #333;"><span class="idiff">pii</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></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">pvarname</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">nullptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pcp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgr_alloc_cacheline_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">xheader</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgfi</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2532" class="line" lang="cpp"> <span class="p">}</span></span>
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2533
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2533
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<pre style="margin: 0;"> <span id="LC2533" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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2534
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2534
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<pre style="margin: 0;"> <span id="LC2534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink2Core_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2538" style="width: 35px; color: rgba(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">@@ -2538,7 +2538,7 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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2538
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<pre style="margin: 0;"> <span id="LC2538" class="line" lang="cpp"> <span class="p">}</span></span>
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2539
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2539
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<pre style="margin: 0;"> <span id="LC2539" class="line" lang="cpp"></span>
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2540
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2540
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<pre style="margin: 0;"> <span id="LC2540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">command_flags1</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfCommand1Exportf</span><span class="p">)</span> <span class="p">{</span></span>
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2541
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<pre style="margin: 0;">-<span id="LC2541" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Exportf</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pii</span><span class="p">,</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_qual_present</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_quals</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_npass</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_storage</span><span class="p">,</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pvarname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exportf_info</span><span class="p">),</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_variant_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">make_plink2_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pgr_alloc_cacheline_ct</span><span class="p">,</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgfi</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2541" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Exportf</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pii</span><span class="p">,</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_qual_present</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_quals</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_npass</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_filter_storage</span><span class="p">,</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pvarname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exportf_info</span><span class="p">),</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_variant_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">pcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">make_plink2_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pgr_alloc_cacheline_ct</span><span class="p">,</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgfi</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">simple_pgr</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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2542
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2542
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<pre style="margin: 0;"> <span id="LC2542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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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
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2543
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<pre style="margin: 0;"> <span id="LC2543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink2Core_ret_1</span><span class="p">;</span></span>
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2544
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2544
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<pre style="margin: 0;"> <span id="LC2544" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5943" style="width: 35px; color: rgba(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">@@ -5943,8 +5943,19 @@ int main(int argc, char** argv) {</td>
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5943
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5943
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<pre style="margin: 0;"> <span id="LC5943" class="line" lang="cpp"> <span class="p">}</span></span>
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5944
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5944
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<pre style="margin: 0;"> <span id="LC5944" class="line" lang="cpp"> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">filter_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfFilterPsamReq</span><span class="p">;</span></span>
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5945
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<td class="diff-line-num new_line" data-linenumber="5945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5945
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<pre style="margin: 0;"> <span id="LC5945" class="line" lang="cpp"> <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;">strequal_k_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">flagname_p2</span><span class="p">,</span> <span class="s" style="color: #d14;">"eep-autoconv"</span><span class="p">))</span> <span class="p">{</span></span>
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5946
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<pre style="margin: 0;">+<span id="LC5946" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">EnforceParamCtRange</span><span class="p">(</span><span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span><span class="p">],</span> <span class="n" style="color: #333;">param_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)))</span> <span class="p">{</span></span>
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5947
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<pre style="margin: 0;">+<span id="LC5947" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_2A</span><span class="p">;</span></span>
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5948
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<pre style="margin: 0;">+<span id="LC5948" class="line" lang="cpp"> <span class="p">}</span></span>
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5949
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<pre style="margin: 0;">+<span id="LC5949" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">param_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5950" 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">
5950
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<pre style="margin: 0;">+<span id="LC5950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_modif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5951" 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">
5951
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<pre style="margin: 0;">+<span id="LC5951" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likely</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;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vzs"</span><span class="p">)))</span> <span class="p">{</span></span>
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5952
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<pre style="margin: 0;">+<span id="LC5952" class="line" lang="cpp"> <span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfImportKeepAutoconvVzs</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5953" 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">
5953
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<pre style="margin: 0;">+<span id="LC5953" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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5954
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<pre style="margin: 0;">+<span id="LC5954" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Invalid --keep-autoconv argument '%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;">cur_modif</span><span class="p">);</span></span>
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5955
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<pre style="margin: 0;">+<span id="LC5955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_WWA</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5946" 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="5956" 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">
5956
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<pre style="margin: 0;">+<span id="LC5956" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5946" 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="5957" 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">
5957
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<pre style="margin: 0;">+<span id="LC5957" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="5946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5946
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<td class="diff-line-num new_line" data-linenumber="5958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5958
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<pre style="margin: 0;"> <span id="LC5958" class="line" lang="cpp"> <span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfImportKeepAutoconv</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5947" 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">
5947
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<td class="diff-line-num new_line old" data-linenumber="5959" 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="LC5947" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_param_zero</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5948
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<td class="diff-line-num new_line" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5959
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<pre style="margin: 0;"> <span id="LC5959" class="line" lang="cpp"> <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;">strequal_k_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">flagname_p2</span><span class="p">,</span> <span class="s" style="color: #d14;">"eep-females"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5949
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<td class="diff-line-num new_line" data-linenumber="5960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5960
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<pre style="margin: 0;"> <span id="LC5960" class="line" lang="cpp"> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">filter_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfFilterPsamReq</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfFilterExclMales</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfFilterExclNosex</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5950
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<td class="diff-line-num new_line" data-linenumber="5961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5961
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<pre style="margin: 0;"> <span id="LC5961" class="line" lang="cpp"> <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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6424" style="width: 35px; color: rgba(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="6435" style="width: 35px; color: rgba(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">@@ -6424,12 +6435,12 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="6424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6424
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<td class="diff-line-num new_line" data-linenumber="6435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6435
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<pre style="margin: 0;"> <span id="LC6435" class="line" lang="cpp"> <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>
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<td class="diff-line-num old_line" data-linenumber="6425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6425
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<td class="diff-line-num new_line" data-linenumber="6436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6436
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<pre style="margin: 0;"> <span id="LC6436" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6426
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<td class="diff-line-num new_line" data-linenumber="6437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6437
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<pre style="margin: 0;"> <span id="LC6437" class="line" lang="cpp"> <span class="n" style="color: #333;">explicit_pvar_cols</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="6427" 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">
6427
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<td class="diff-line-num new_line old" data-linenumber="6438" 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="LC6427" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseColDescriptor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"pvar-cols="</span><span class="p">)]),</span> <span class="s" style="color: #d14;">"xheader</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybequal</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">qual</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybefilter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">filter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybeinfo</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">info</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybecm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">cm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--make-pgen pvar-cols"</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColDefault</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6428" 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="6438" 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">
6438
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<pre style="margin: 0;">+<span id="LC6438" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseColDescriptor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"pvar-cols="</span><span class="p">)]),</span> <span class="s" style="color: #d14;">"xheader</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;"><span class="idiff left">vcfheader</span></span><span class="se" style="color: #d14;"><span class="idiff right">\0</span></span><span class="s" style="color: #d14;">maybequal</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">qual</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybefilter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">filter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybeinfo</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">info</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybecm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">cm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--make-pgen pvar-cols"</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColDefault</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6428
</td>
<td class="diff-line-num new_line" data-linenumber="6439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6439
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6429
</td>
<td class="diff-line-num new_line" data-linenumber="6440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6440
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6430
</td>
<td class="diff-line-num new_line" data-linenumber="6441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6441
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6441" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6431" 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">
6431
</td>
<td class="diff-line-num new_line old" data-linenumber="6442" 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="LC6431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXinfo</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="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;"><span class="idiff left right">kfPvarColXheader</span></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="6432" 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">
6432
</td>
<td class="diff-line-num new_line old" data-linenumber="6442" 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="LC6432" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen pvar-cols= expression cannot exclude xheader<span class="idiff left"> when info is</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6433" 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="6442" 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">
6442
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<pre style="margin: 0;">+<span id="LC6442" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXinfo</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="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">kfPvarColXheader</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">kfPvarColVcfheader</span></span><span class="p"><span class="idiff right">)</span>))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6433" 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="6443" 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">
6443
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<pre style="margin: 0;">+<span id="LC6443" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen pvar-cols= expression cannot exclude xheader<span class="idiff left">/vcfheader when</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">info is </span>present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6433
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<td class="diff-line-num new_line" data-linenumber="6444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6444
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<pre style="margin: 0;"> <span id="LC6444" class="line" lang="cpp"> <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>
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<td class="diff-line-num old_line" data-linenumber="6434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6434
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<td class="diff-line-num new_line" data-linenumber="6445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6445
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<pre style="margin: 0;"> <span id="LC6445" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6435
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<td class="diff-line-num new_line" data-linenumber="6446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6446
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<pre style="margin: 0;"> <span id="LC6446" class="line" lang="cpp"> <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;">StrStartsWith</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"format="</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6585" style="width: 35px; color: rgba(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="6596" style="width: 35px; color: rgba(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">@@ -6585,12 +6596,12 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="6585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6585
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<td class="diff-line-num new_line" data-linenumber="6596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6596
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<pre style="margin: 0;"> <span id="LC6596" class="line" lang="cpp"> <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>
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<td class="diff-line-num old_line" data-linenumber="6586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6586
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<td class="diff-line-num new_line" data-linenumber="6597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6597
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<pre style="margin: 0;"> <span id="LC6597" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6587
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<td class="diff-line-num new_line" data-linenumber="6598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6598
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<pre style="margin: 0;"> <span id="LC6598" class="line" lang="cpp"> <span class="n" style="color: #333;">explicit_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6588" 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">
6588
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<td class="diff-line-num new_line old" data-linenumber="6599" 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="LC6588" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseColDescriptor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]),</span> <span class="s" style="color: #d14;">"xheader</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybequal</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">qual</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybefilter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">filter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybeinfo</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">info</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybecm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">cm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"make-just-pvar"</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColDefault</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6589" 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="6599" 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">
6599
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<pre style="margin: 0;">+<span id="LC6599" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseColDescriptor</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]),</span> <span class="s" style="color: #d14;">"xheader</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;"><span class="idiff left">vcfheader</span></span><span class="se" style="color: #d14;"><span class="idiff right">\0</span></span><span class="s" style="color: #d14;">maybequal</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">qual</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybefilter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">filter</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybeinfo</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">info</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">maybecm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">cm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"make-just-pvar"</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">,</span> <span class="n" style="color: #333;">kfPvarColDefault</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6589
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<td class="diff-line-num new_line" data-linenumber="6600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6600
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<pre style="margin: 0;"> <span id="LC6600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6590
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<td class="diff-line-num new_line" data-linenumber="6601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6601
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<pre style="margin: 0;"> <span id="LC6601" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6591
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<td class="diff-line-num new_line" data-linenumber="6602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6602
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<pre style="margin: 0;"> <span id="LC6602" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6592" 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">
6592
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<td class="diff-line-num new_line old" data-linenumber="6603" 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="LC6592" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXinfo</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="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;"><span class="idiff left right">kfPvarColXheader</span></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="6593" 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">
6593
</td>
<td class="diff-line-num new_line old" data-linenumber="6603" 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="LC6593" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-just-pvar cols= expression cannot exclude xheader<span class="idiff left"> when info is</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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6603
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<pre style="margin: 0;">+<span id="LC6603" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXinfo</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="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">kfPvarColXheader</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">kfPvarColVcfheader</span></span><span class="p"><span class="idiff right">)</span>))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6604" 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">
6604
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<pre style="margin: 0;">+<span id="LC6604" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-just-pvar cols= expression cannot exclude xheader<span class="idiff left">/vcfheader when</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">info is </span>present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6594
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6605
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<pre style="margin: 0;"> <span id="LC6605" class="line" lang="cpp"> <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>
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<td class="diff-line-num old_line" data-linenumber="6595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6595
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<td class="diff-line-num new_line" data-linenumber="6606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6606
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<pre style="margin: 0;"> <span id="LC6606" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6596
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<td class="diff-line-num new_line" data-linenumber="6607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6607
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<pre style="margin: 0;"> <span id="LC6607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColInfo</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9858" style="width: 35px; color: rgba(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="9869" style="width: 35px; color: rgba(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">@@ -9858,29 +9869,53 @@ int main(int argc, char** argv) {</td>
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9858
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<td class="diff-line-num new_line" data-linenumber="9869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9869
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<pre style="margin: 0;"> <span id="LC9869" class="line" lang="cpp"> <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;">convname_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convname_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">outname</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9859
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<td class="diff-line-num new_line" data-linenumber="9870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9870
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<pre style="margin: 0;"> <span id="LC9870" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pgen_generated</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9860
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<td class="diff-line-num new_line" data-linenumber="9871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9871
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<pre style="margin: 0;"> <span id="LC9871" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">psam_generated</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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9872
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<pre style="margin: 0;">+<span id="LC9872" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="9873" 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">
9873
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<pre style="margin: 0;">+<span id="LC9873" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Compress by default for VCF/BCF due to potentially large INFO</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9861" 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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9874
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<pre style="margin: 0;">+<span id="LC9874" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// section; otherwise only do it in "--keep-autoconv vzs" case.</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9861" 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="9875" 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">
9875
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<pre style="margin: 0;">+<span id="LC9875" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pvar_is_compressed</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9861
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<td class="diff-line-num new_line" data-linenumber="9876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9876
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<pre style="margin: 0;"> <span id="LC9876" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfXloadVcf</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfXloadBcf</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9862
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<td class="diff-line-num new_line" data-linenumber="9877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9877
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<pre style="margin: 0;"> <span id="LC9877" class="line" lang="cpp"> <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;">no_samples_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dependency_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfFilterAllReq</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfFilterPsamReq</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="9863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9863
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<td class="diff-line-num new_line" data-linenumber="9878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9878
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<pre style="margin: 0;"> <span id="LC9878" class="line" lang="cpp"> <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;">is_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">xload</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfXloadVcf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9864" 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="9879" 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">
9879
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<pre style="margin: 0;">+<span id="LC9879" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_is_compressed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfImportKeepAutoconv</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfImportKeepAutoconvVzs</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kfImportKeepAutoconv</span><span class="p">);</span></span>
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9864
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<td class="diff-line-num new_line" data-linenumber="9880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9880
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<pre style="margin: 0;"> <span id="LC9880" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">no_samples_ok</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">is_vcf</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfImportKeepAutoconv</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">command_flags1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9865
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<td class="diff-line-num new_line" data-linenumber="9881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9881
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<pre style="margin: 0;"> <span id="LC9881" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// special case: just treat the VCF as a .pvar file</span></span>
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9866
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9882
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<pre style="margin: 0;"> <span id="LC9882" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">pgenname</span><span class="p">);</span></span>
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9867
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9883
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<pre style="margin: 0;"> <span id="LC9883" class="line" lang="cpp"> <span class="n" style="color: #333;">pgenname</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;">'\0'</span><span class="p">;</span></span>
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9868
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9884
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<pre style="margin: 0;"> <span id="LC9884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_reinterpret_vcf_instead_of_converting</span><span class="p">;</span></span>
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9869
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<pre style="margin: 0;">-<span id="LC9869" class="line" lang="cpp"> <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;">is_vcf</span><span class="p">)</span> <span class="p">{</span></span>
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9885
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<pre style="margin: 0;">+<span id="LC9885" class="line" lang="cpp"> <span class="p">}</span></span>
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9886
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<pre style="margin: 0;">+<span id="LC9886" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Default to compression level 1 for temporary .pvar files for now.</span></span>
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9887
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<pre style="margin: 0;">+<span id="LC9887" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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9888
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<pre style="margin: 0;">+<span id="LC9888" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Level 1 may actually be best in a much wider variety of scenarios</span></span>
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9889
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<pre style="margin: 0;">+<span id="LC9889" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// as of this writing, but I won't try to tune any other compression</span></span>
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9890
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<pre style="margin: 0;">+<span id="LC9890" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// defaults for now. Interestingly, the current setup is actually a</span></span>
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9891
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<pre style="margin: 0;">+<span id="LC9891" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bit backwards given observed zstd behavior: the long INFO fields</span></span>
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9892
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<pre style="margin: 0;">+<span id="LC9892" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// motivating automatic compression here are best handled with level</span></span>
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9893
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<pre style="margin: 0;">+<span id="LC9893" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 3, while the other simpler text files generated by plink2 are</span></span>
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9894
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<pre style="margin: 0;">+<span id="LC9894" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// likely to compress *better*, not just faster, with level 1 for</span></span>
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9895
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<pre style="margin: 0;">+<span id="LC9895" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// some reason.</span></span>
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9896
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<pre style="margin: 0;">+<span id="LC9896" class="line" lang="cpp"> <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;">zst_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_zst_level</span><span class="p">;</span></span>
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9897
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<pre style="margin: 0;">+<span id="LC9897" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfImportKeepAutoconv</span><span class="p">))</span> <span class="p">{</span></span>
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9898
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<pre style="margin: 0;">+<span id="LC9898" class="line" lang="cpp"> <span class="n" style="color: #333;">g_zst_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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9899
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<pre style="margin: 0;">+<span id="LC9899" class="line" lang="cpp"> <span class="p">}</span></span>
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9900
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<pre style="margin: 0;">+<span id="LC9900" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_vcf</span><span class="p">)</span> <span class="p">{</span></span>
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9870
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9901
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<pre style="margin: 0;"> <span id="LC9901" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VcfToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">load_params</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfLoadParamsPsam</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">psamname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">const_fid</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_dosage_import_field</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">no_samples_ok</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">,</span> <span class="n" style="color: #333;">idspace_to</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_min_gq</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_min_dp</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_max_dp</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_half_call</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgen_generated</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">psam_generated</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="9871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9871
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<td class="diff-line-num new_line" data-linenumber="9902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9902
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<pre style="margin: 0;"> <span id="LC9902" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9872
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<td class="diff-line-num new_line" data-linenumber="9903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9903
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<pre style="margin: 0;"> <span id="LC9903" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BcfToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">load_params</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfLoadParamsPsam</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">psamname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">const_fid</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_dosage_import_field</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">no_samples_ok</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">,</span> <span class="n" style="color: #333;">idspace_to</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_min_gq</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_min_dp</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_max_dp</span><span class="p">,</span> <span class="n" style="color: #333;">vcf_half_call</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgen_generated</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">psam_generated</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="9873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9873
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<td class="diff-line-num new_line" data-linenumber="9904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9904
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<pre style="margin: 0;"> <span id="LC9904" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9874" 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">
9874
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9874" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxGen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9875" 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">
9875
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9875" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxGenToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9876" 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">
9876
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9876" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxBgen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9877" 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">
9877
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9877" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxBgenToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">const_fid</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">,</span> <span class="n" style="color: #333;">idspace_to</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9878" 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">
9878
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9878" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxHaps</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9879" 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">
9879
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9879" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxHapslegendToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9880" 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">
9880
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9880" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadPlink1Dosage</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="9881" 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">
9881
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9881" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Plink1DosageToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadMap</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pvarname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">plink1_dosage_info</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">missing_pheno</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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9882
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9882" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadGenDummy</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9883" 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">
9883
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<td class="diff-line-num new_line old" data-linenumber="9905" 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="LC9883" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenerateDummy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gendummy_info</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">main_sfmt</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9905" 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">
9905
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<pre style="margin: 0;">+<span id="LC9905" class="line" lang="cpp"> <span class="n" style="color: #333;">g_zst_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zst_level</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9906" 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">
9906
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<pre style="margin: 0;">+<span id="LC9906" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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9907
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<pre style="margin: 0;">+<span id="LC9907" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_is_compressed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">import_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfImportKeepAutoconvVzs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9908" 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">
9908
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<pre style="margin: 0;">+<span id="LC9908" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxGen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9909" 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">
9909
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<pre style="margin: 0;">+<span id="LC9909" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxGenToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9910" 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">
9910
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<pre style="margin: 0;">+<span id="LC9910" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxBgen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9911" 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">
9911
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<pre style="margin: 0;">+<span id="LC9911" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxBgenToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">const_fid</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">,</span> <span class="n" style="color: #333;">idspace_to</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9912" 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">
9912
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<pre style="margin: 0;">+<span id="LC9912" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadOxHaps</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9913" 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">
9913
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<pre style="margin: 0;">+<span id="LC9913" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OxHapslegendToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="n" style="color: #333;">ox_missing_code</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">oxford_import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9914" 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">
9914
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<pre style="margin: 0;">+<span id="LC9914" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadPlink1Dosage</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9915" 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">
9915
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<pre style="margin: 0;">+<span id="LC9915" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Plink1DosageToPgen</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadMap</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pvarname</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">import_single_chr_str</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">plink1_dosage_info</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">missing_pheno</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">import_dosage_certainty</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9916" 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">
9916
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<pre style="margin: 0;">+<span id="LC9916" class="line" lang="cpp"> <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;">xload</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfXloadGenDummy</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9884" 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="9917" 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">
9917
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<pre style="margin: 0;">+<span id="LC9917" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenerateDummy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gendummy_info</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">import_flags</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">,</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">main_sfmt</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_info</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9918" 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">
9918
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<pre style="margin: 0;">+<span id="LC9918" class="line" lang="cpp"> <span class="p">}</span></span>
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9884
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<td class="diff-line-num new_line" data-linenumber="9919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9919
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<pre style="margin: 0;"> <span id="LC9919" class="line" lang="cpp"> <span class="p">}</span></span>
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9885
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<td class="diff-line-num new_line" data-linenumber="9920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9920
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<pre style="margin: 0;"> <span id="LC9920" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reterr</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;">pc</span><span class="p">.</span><span class="n" style="color: #333;">command_flags1</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9886
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<td class="diff-line-num new_line" data-linenumber="9921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9921
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<pre style="margin: 0;"> <span id="LC9921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9893" style="width: 35px; color: rgba(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="9928" style="width: 35px; color: rgba(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">@@ -9893,7 +9928,7 @@ int main(int argc, char** argv) {</td>
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9893
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9928
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<pre style="margin: 0;"> <span id="LC9928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pgen_generated</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9894
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<td class="diff-line-num new_line" data-linenumber="9929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9929
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<pre style="margin: 0;"> <span id="LC9929" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_slen</span><span class="p">),</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="s" style="color: #d14;">".pgen"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="9895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9895
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<td class="diff-line-num new_line" data-linenumber="9930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9930
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<pre style="margin: 0;"> <span id="LC9930" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9896" 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">
9896
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<td class="diff-line-num new_line old" data-linenumber="9931" 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="LC9896" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_slen</span><span class="p">),</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="s" style="color: #d14;">".pvar"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9897" 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="9931" 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">
9931
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<pre style="margin: 0;">+<span id="LC9931" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_slen</span><span class="p">),</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">pvar_is_compressed</span></span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">".pvar.zst"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">".pvar"</span><span class="p">);</span></span>
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9897
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<td class="diff-line-num new_line" data-linenumber="9932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9932
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<pre style="margin: 0;"> <span id="LC9932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">psam_generated</span><span class="p">)</span> <span class="p">{</span></span>
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9898
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<td class="diff-line-num new_line" data-linenumber="9933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9933
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<pre style="margin: 0;"> <span id="LC9933" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">convname_slen</span><span class="p">),</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">);</span></span>
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9899
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<td class="diff-line-num new_line" data-linenumber="9934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9934
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<pre style="margin: 0;"> <span id="LC9934" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#5c0ac48ba397674ac28142efc3b29b7de442d076"><strong>plink2_cmdline.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3856" style="width: 35px; color: rgba(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="3856" style="width: 35px; color: rgba(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">@@ -3856,6 +3856,10 @@ PglErr CmdlineParsePhase2(const char* ver_str, const char* errstr_append, const</td>
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3856
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3856
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<pre style="margin: 0;"> <span id="LC3856" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flag_map</span><span class="p">[</span><span class="n" style="color: #333;">cur_flag_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3857
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3857
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<pre style="margin: 0;"> <span id="LC3857" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">S_CAST</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;">argc</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;">IsCmdlineFlag</span><span class="p">(</span><span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span><span class="p">])))</span> <span class="p">{</span></span>
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3858
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3858
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<pre style="margin: 0;"> <span id="LC3858" class="line" lang="cpp"> <span class="n" style="color: #333;">logputs</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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3859
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<pre style="margin: 0;">+<span id="LC3859" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Thought about special-casing argvk[arg_idx] == " ", so that</span></span>
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3860
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<pre style="margin: 0;">+<span id="LC3860" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// "--id-delim ' '" actually works with --rerun, but that adds too much</span></span>
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3861
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<pre style="margin: 0;">+<span id="LC3861" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// complexity to the rereader to be worth it. Instead we just document</span></span>
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3862
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<pre style="margin: 0;">+<span id="LC3862" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the incompatibility.</span></span>
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3859
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3863
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<pre style="margin: 0;"> <span id="LC3863" class="line" lang="cpp"> <span class="n" style="color: #333;">logputs</span><span class="p">(</span><span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">]);</span></span>
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3860
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3864
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<pre style="margin: 0;"> <span id="LC3864" class="line" lang="cpp"> <span class="p">}</span></span>
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3861
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3865
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<pre style="margin: 0;"> <span id="LC3865" class="line" lang="cpp"> <span class="n" style="color: #333;">logputs</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#353424a9b88ab7aad403c3734bdd60f28af6b661"><strong>plink2_cmdline.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1761,12 +1761,35 @@ typedef struct CmpExprStruct {</td>
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1761
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1761
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<pre style="margin: 0;"> <span id="LC1761" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// arguably too small for noncopyable to be a great idea, but the next</span></span>
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1762
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1762
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<pre style="margin: 0;"> <span id="LC1762" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// iteration of this struct probably won't have that issue.</span></span>
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1763
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<pre style="margin: 0;"> <span id="LC1763" class="line" lang="cpp"> <span class="n" style="color: #333;">NONCOPYABLE</span><span class="p">(</span><span class="n" style="color: #333;">CmpExprStruct</span><span class="p">);</span></span>
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1764
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<pre style="margin: 0;">-<span id="LC1764" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Restrict to [pheno/covar name] [operator] [pheno val] for now. could</span></span>
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1765
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<pre style="margin: 0;">-<span id="LC1765" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// support or/and, parentheses, etc. later.</span></span>
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1766
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<pre style="margin: 0;">-<span id="LC1766" class="line" lang="cpp"></span>
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1767
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<pre style="margin: 0;">-<span id="LC1767" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Currently stores null-terminated pheno/covar name, followed by</span></span>
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1768
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<pre style="margin: 0;">-<span id="LC1768" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// null-terminated value string. Storage format needs to be synced with</span></span>
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1769
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<pre style="margin: 0;">-<span id="LC1769" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ValidateAndAllocCmpExpr().</span></span>
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1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Restrict to <key> <operator> <value> for now; key=INFO/pheno/covar.</span></span>
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1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1766" 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">
1766
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<pre style="margin: 0;">+<span id="LC1766" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Almost certainly want to support conjunctions/disjunctions later; but</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1767" 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">
1767
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<pre style="margin: 0;">+<span id="LC1767" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there are complications regarding the command-line interface:</span></span>
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1768
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<pre style="margin: 0;">+<span id="LC1768" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// * Phenotype/covariate names and VCFv4.2 INFO keys can contain parenthesis</span></span>
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1769
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<pre style="margin: 0;">+<span id="LC1769" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and mathematical-operator characters. And we actually need to permit at</span></span>
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1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// least the latter, since autogenerated categorical-covariate names</span></span>
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1771
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<pre style="margin: 0;">+<span id="LC1771" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// contain '=' for a good reason. Some sort of escaping is probably in</span></span>
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1772
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<pre style="margin: 0;">+<span id="LC1772" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in order, but...</span></span>
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1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// * Escaping is not a big deal in a shell script, but most</span></span>
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1774
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<pre style="margin: 0;">+<span id="LC1774" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// conjunctions/disjunctions can already be emulated easily enough in a</span></span>
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1775
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<pre style="margin: 0;">+<span id="LC1775" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// shell script by calling plink2 multiple times. While there's some</span></span>
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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// execution-time improvement, the main value-add from directly supporting</span></span>
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1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// logical operations in --keep-if/--extract-if-info is reduced</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1778" 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">
1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// interactive-use cognitive load.</span></span>
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1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// * We can't treat multiple command-line arguments differently from the</span></span>
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1780
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<pre style="margin: 0;">+<span id="LC1780" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// corresponding space-containing single command-line argument; otherwise</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1781" 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">
1781
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<pre style="margin: 0;">+<span id="LC1781" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --rerun breaks. So "multiple-argument-form supports keys with special</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1782" 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">
1782
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<pre style="margin: 0;">+<span id="LC1782" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// characters but not conjunctions/disjunctions; single-argument-form is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1783" 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">
1783
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<pre style="margin: 0;">+<span id="LC1783" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the other way around" is not an option.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1784" 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">
1784
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<pre style="margin: 0;">+<span id="LC1784" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The least-bad solution I've thought of is to add --keep-if-file/etc. flags</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1785" 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">
1785
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<pre style="margin: 0;">+<span id="LC1785" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// which read the expression from a short text file. In that case, we'd at</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1786" 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">
1786
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<pre style="margin: 0;">+<span id="LC1786" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// least be able to define normal quoting and escaping rules without worrying</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1787" 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">
1787
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<pre style="margin: 0;">+<span id="LC1787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// about confusing interactions with bash. Deferring implementation for now</span></span>
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1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in hopes of coming up with a better idea, but this should go in before</span></span>
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1789
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// beta testing begins.</span></span>
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1790
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<pre style="margin: 0;">+<span id="LC1790" class="line" lang="cpp"></span>
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1791
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<pre style="margin: 0;">+<span id="LC1791" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Currently stores null-terminated key, followed by null-terminated value</span></span>
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1792
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<pre style="margin: 0;">+<span id="LC1792" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// string. Storage format needs to be synced with ValidateAndAllocCmpExpr().</span></span>
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1770
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1793
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_name</span><span class="p">;</span></span>
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1771
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1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="cpp"> <span class="n" style="color: #333;">CmpBinaryOp</span> <span class="n" style="color: #333;">binary_op</span><span class="p">;</span></span>
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1772
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1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">CmpExpr</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -260,6 +260,56 @@ void PopulateRescaledDosage(const uintptr_t* genoarr, const uintptr_t* dosage_pr</td>
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260
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="p">}</span></span>
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261
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"><span class="p">}</span></span>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static_assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</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="s" style="color: #d14;">"AtLeastOneMultiallelicHet() needs to be updated."</span><span class="p">);</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">AtLeastOneMultiallelicHet</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PgenVariant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgvp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pgvp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patch_01_ct</span><span class="p">)</span> <span class="p">{</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="p">}</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="p">{</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pgvp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">genovec</span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <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;">fullvec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">;</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fullvec_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Word01</span><span class="p">(</span><span class="n" style="color: #333;">geno_word</span><span class="p">))</span> <span class="p">{</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <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;">remainder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">remainder</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Word01</span><span class="p">(</span><span class="n" style="color: #333;">bzhi</span><span class="p">(</span><span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">fullvec_ct</span><span class="p">],</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">remainder</span><span class="p">)))</span> <span class="p">{</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="p">}</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="p">}</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <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;">patch_10_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pgvp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patch_10_ct</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">patch_10_ct</span><span class="p">)</span> <span class="p">{</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlleleCode</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">patch_10_vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pgvp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patch_10_vals</span><span class="p">;</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LP64__</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <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;">fullvec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patch_10_ct</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kBytesPerVec</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">patch_10_valias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">patch_10_vals</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">m8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecu16_set1</span><span class="p">(</span><span class="mh" style="color: #099;">0xff</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" 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">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <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;">vidx</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;">vidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fullvec_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vidx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vv_orig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecu16_loadu</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">patch_10_valias</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">]));</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vv_hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vecu16_srli</span><span class="p">(</span><span class="n" style="color: #333;">vv_orig</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vv_lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vv_orig</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">m8</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecU16</span> <span class="n" style="color: #333;">vv_eq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">vv_hi</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">vv_lo</span><span class="p">);</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vecu16_movemask</span><span class="p">(</span><span class="n" style="color: #333;">vv_eq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kVec8thUintMax</span><span class="p">)</span> <span class="p">{</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="p">}</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fullvec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">kBytesPerVec</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">uii</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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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">patch_10_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">patch_10_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">uii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">patch_10_vals</span><span class="p">[</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="p">}</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="p">}</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"><span class="p">}</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"></span>
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263
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetHetMissing</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">word_ct</span><span class="p">,</span> <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;">genovec</span><span class="p">)</span> <span class="p">{</span></span>
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264
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 01 -> 11, nothing else changes</span></span>
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265
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __LP64__</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1451" style="width: 35px; color: rgba(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">@@ -1401,9 +1451,8 @@ char* ChrNameStd(const ChrInfo* cip, uint32_t chr_idx, char* buf) {</td>
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1401
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1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chrtoa</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="p">{</span></span>
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1402
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1452
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<pre style="margin: 0;"> <span id="LC1452" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assumes chr_idx is valid</span></span>
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1403
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1453
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="cpp"> <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;">chr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: probably add 'chr' in front here when output encoding calls for</span></span>
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1405
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<pre style="margin: 0;">-<span id="LC1405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// it, but wait till beta since this would technically be</span></span>
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1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// compatibility-breaking</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Note that this never has a 'chr' prefix. Which is probably fine, it</span></span>
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1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// isn't a real chromosome.</span></span>
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1407
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1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">;</span></span>
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1408
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1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">buf</span><span class="p">;</span></span>
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1409
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1581" style="width: 35px; color: rgba(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="1630" style="width: 35px; color: rgba(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">@@ -1581,9 +1630,12 @@ uint32_t GetChrCode(const char* chr_name, const ChrInfo* cip, uint32_t name_slen</td>
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1581
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1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="cpp"><span class="p">}</span></span>
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1582
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1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="cpp"></span>
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1583
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1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetChrCodeCounted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">name_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name</span><span class="p">)</span> <span class="p">{</span></span>
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1584
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<pre style="margin: 0;">-<span id="LC1584" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// when the chromosome name isn't null-terminated</span></span>
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1585
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<pre style="margin: 0;">-<span id="LC1585" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (yeah, probably want to revise the called functions so that chr_name</span></span>
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1586
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<pre style="margin: 0;">-<span id="LC1586" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// doesn't need to be mutable here)</span></span>
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1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// When the chromosome name isn't null-terminated.</span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Yeah, probably want to revise this so that chr_name doesn't need to be</span></span>
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mutable here. However, that currently requires new substitutes for both</span></span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// GetChrCodeRaw AND IdHtableFind (IdHtableFindNnt doesn't work due to</span></span>
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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// overread); when either of those are needed for some other reason, that's a</span></span>
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1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// good time to revise this function.</span></span>
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1587
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1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">chr_name</span><span class="p">[</span><span class="n" style="color: #333;">name_slen</span><span class="p">]);</span></span>
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1588
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1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="cpp"> <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;">tmpc</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_end</span><span class="p">;</span></span>
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1589
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1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#576e4fd14d1d66b779bb9f5d05d29f2871392d1a"><strong>plink2_common.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,26 +201,27 @@ FLAGSET_DEF_START()</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarZs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColXheader</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybequal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</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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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybefilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybeinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">6</span><span class="p">),</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColInfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">7</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColVcfheader</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybequal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</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="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybefilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">6</span><span class="p">),</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybeinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">7</span><span class="p">),</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColInfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">8</span><span class="p">),</span></span>
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210
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColXinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">kfPvarColInfo</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfPvarColMaybeinfo</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybecm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;"><span class="idiff left right">8</span></span><span class="p">),</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColCm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">),</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColMaybecm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">),</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColCm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;"><span class="idiff left right">10</span></span><span class="p">),</span></span>
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213
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColDefault</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">kfPvarColXheader</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColMaybequal</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColMaybefilter</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColMaybeinfo</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColMaybecm</span><span class="p">),</span></span>
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214
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPvarColAll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">kfPvarColCm</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">),</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybefid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">0</span></span><span class="p">),</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColFid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">1</span></span><span class="p">),</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybesid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">2</span></span><span class="p">),</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColSid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">3</span></span><span class="p">),</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybeparents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">4</span></span><span class="p">),</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColParents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">5</span></span><span class="p">),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColSex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">6</span></span><span class="p">),</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColPheno1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">7</span></span><span class="p">),</span></span>
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<td class="diff-line-num old old_line" data-linenumber="223" 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">
223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColPhenos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">8</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybefid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">1</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColFid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">2</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybesid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">3</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColSid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">4</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColMaybeparents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">5</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColParents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">6</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColSex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">7</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColPheno1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">8</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColPhenos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1<span class="idiff left right">9</span></span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColDefault</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">kfPsamColMaybefid</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPsamColMaybesid</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPsamColMaybeparents</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPsamColSex</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPsamColPhenos</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColAll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">kfPsamColPhenos</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfPsamColMaybefid</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">PvarPsamFlags</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -382,6 +383,20 @@ void PopulateDenseDosage(const uintptr_t* genoarr, const uintptr_t* dosage_prese</td>
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382
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"></span>
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383
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PopulateRescaledDosage</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">dosage_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Dosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dosage_main</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">slope</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">intercept</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">missing_val</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">dosage_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">expanded_dosages</span><span class="p">);</span></span>
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384
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes trailing bits of genoarr are zeroed out</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">AtLeastOneHetUnsafe</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">genoarr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <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;">sample_ctl2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ctl2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoarr</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">];</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Word01</span><span class="p">(</span><span class="n" style="color: #333;">geno_word</span><span class="p">))</span> <span class="p">{</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="p">}</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"><span class="p">}</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">AtLeastOneMultiallelicHet</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PgenVariant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgvp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">);</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"></span>
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385
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetHetMissing</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">word_ct</span><span class="p">,</span> <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;">genovec</span><span class="p">);</span></span>
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386
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"></span>
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387
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetHetMissingCleardosage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">word_ct</span><span class="p">,</span> <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;">genovec</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_dosage_ct_ptr</span><span class="p">,</span> <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;">dosagepresent</span><span class="p">,</span> <span class="n" style="color: #333;">Dosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dosage_main</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="691" style="width: 35px; color: rgba(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">@@ -691,6 +706,7 @@ PglErr FinalizeChrInfo(ChrInfo* cip);</td>
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691
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CleanupChrInfo</span><span class="p">(</span><span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">);</span></span>
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692
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"></span>
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693
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes chr_idx is valid</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// note that chr_idx == 0 is always rendered as '0', never 'chr0'</span></span>
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694
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chrtoa</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"></span>
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696
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetMaxChrSlen</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1084" style="width: 35px; color: rgba(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">@@ -1068,6 +1084,17 @@ HEADER_INLINE BoolErr StoreStringAtEndK(unsigned char* arena_bottom, const char*</td>
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1068
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1069
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="cpp"><span class="p">}</span></span>
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1070
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="cpp"></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">StoreStringAndPrecharAtEnd</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">prechar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">dst</span><span class="p">)</span> <span class="p">{</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PtrWSubCk</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">))</span> <span class="p">{</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="p">}</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">arena_top_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prechar</span><span class="p">;</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dst_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_top_ptr</span><span class="p">);</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">dst_write</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_write</span><span class="p">;</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"><span class="p">}</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"></span>
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1071
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// These use g_textbuf.</span></span>
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1072
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteSampleIdsOverride</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">SampleIdFlags</span> <span class="n" style="color: #333;">override_flags</span><span class="p">);</span></span>
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1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteSampleIds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,6 +20,8 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_data.h"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_pvar.h"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">plink2</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -266,7 +268,262 @@ void AppendChrsetLine(const ChrInfo* cip, char** write_iter_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">AppendBinaryEoln</span><span class="p">(</span><span class="n" style="color: #333;">write_iter_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvar</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_presents</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">),</span> <span class="k" style="font-weight: 600;">const</span> <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;">qual_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">filter_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">filter_npass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filter_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">nonref_flags</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFlags</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nonref_flags_storage</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="n" style="color: #333;">PvarPsamFlags</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">thread_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// fileformat, fileDate, source</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AppendVcfHeaderStart</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v43</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">)</span> <span class="p">{</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span><span class="p">;</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##fileformat=VCFv4."</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v43</span> <span class="o" style="font-weight: 600;">+</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">;</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="n" style="color: #333;">EOLN_STR</span> <span class="s" style="color: #d14;">"##fileDate="</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">time_t</span> <span class="n" style="color: #333;">rawtime</span><span class="p">;</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">time</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rawtime</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">loctime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localtime</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rawtime</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxMediumLine</span><span class="p">,</span> <span class="s" style="color: #d14;">"%Y%m%d"</span><span class="p">,</span> <span class="n" style="color: #333;">loctime</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="n" style="color: #333;">EOLN_STR</span> <span class="s" style="color: #d14;">"##source=PLINKv2.00"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cswritep</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Note that the order-of-operations page lists this as happening right after</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// the filtering performed by LoadPvar(). Which is effectively true, since we</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ignore variant_include (this is safe since LoadPvar() always initializes</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// all variant_bps[] and allele_storage[] entries appropriately).</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// possible todo: ChrInfo can have a length field, which is initialized by the</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ##contig header line when possible, but when that doesn't exist LoadPvar()</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// can conditionally detect INFO:END and take that into account. (Or a reason</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// to keep the entire info_end array in memory may emerge.)</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ChrLenLbound</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chr_fo_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">UnsortedVar</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">)</span> <span class="p">{</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <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;">vidx_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chr_fo_idx</span><span class="p">];</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <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;">vidx_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chr_fo_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">vidx_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vidx_end</span><span class="p">);</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">vpos_sortstatus</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfUnsortedVarBp</span><span class="p">))</span> <span class="p">{</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <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;">new_variant_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_allele_slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">vidx_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="p">}</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bp_end</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 new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <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;">vidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vidx_end</span><span class="p">;</span> <span class="n" style="color: #333;">vidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vidx_start</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">vidx</span><span class="p">;</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">];</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_allele_slen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bp_end</span><span class="p">)</span> <span class="p">{</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="p">}</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">];</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="p">}</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We only care about reference-allele length.</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">allele_storage</span><span class="p">[</span><span class="n" style="color: #333;">allele_idx_offset_base</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bp_end</span><span class="p">)</span> <span class="p">{</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp_end</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="p">}</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bp_end</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_allele_slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">vidx_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]];</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bp_end</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 new_line" data-linenumber="326" 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">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <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;">new_vidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vidx_end</span><span class="p">;</span> <span class="n" style="color: #333;">new_vidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vidx_start</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">new_vidx</span><span class="p">;</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <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;">old_vidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">new_vidx</span><span class="p">];</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">old_vidx</span><span class="p">];</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_allele_slen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bp_end</span><span class="p">)</span> <span class="p">{</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_vidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">[</span><span class="n" style="color: #333;">old_vidx</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">allele_storage</span><span class="p">[</span><span class="n" style="color: #333;">allele_idx_offset_base</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bp_end</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp_end</span><span class="p">;</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="p">}</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bp_end</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">U32ArrMax</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">vidx_start</span><span class="p">]),</span> <span class="n" style="color: #333;">vidx_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">vidx_start</span><span class="p">);</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_allele_slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bp_end</span><span class="p">;</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_check_bp</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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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">min_check_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">;</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <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;">vidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vidx_start</span><span class="p">;</span> <span class="n" style="color: #333;">vidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vidx_end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">vidx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">];</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_check_bp</span><span class="p">)</span> <span class="p">{</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">)</span> <span class="p">{</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_idx_offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">[</span><span class="n" style="color: #333;">vidx</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">allele_storage</span><span class="p">[</span><span class="n" style="color: #333;">allele_idx_offset_base</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_bp_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bp_end</span><span class="p">)</span> <span class="p">{</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">bp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_bp_end</span><span class="p">;</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="p">}</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bp_end</span><span class="p">;</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"><span class="p">}</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarXheaderWrite</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vcfheader</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_filter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">append_info_pr_header_line</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">UnsortedVar</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">CompressStreamState</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">)</span> <span class="p">{</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="372" 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">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="373" 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">
373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <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;">vcfheader</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">write_info</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="375" 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">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Filter out FILTER/INFO definitions iff the corresponding column has</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// been removed.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xheader</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">[</span><span class="n" style="color: #333;">xheader_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xheader</span><span class="p">;</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_end</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">next_line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <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;">write_filter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FILTER=<ID="</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new old_line" data-linenumber="270" 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="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">write_info</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID="</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_iter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="270" 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="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_line_start</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_line_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="p">}</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="402" 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">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// See the start of ExportVcf().</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">AppendVcfHeaderStart</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <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;">chr_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <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;">written_contig_header_lines</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">chr_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">written_contig_header_lines</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">contig_zero_written</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 new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ExportVcf() has to perform a customized --merge-par operation, so it</span></span>
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<td class="diff-line-num new new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// has special handling of chrX/PAR1/PAR2 ##contig header lines. We omit</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that here.</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">[</span><span class="n" style="color: #333;">xheader_blen</span><span class="p">]);</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xheader</span><span class="p">;</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_end</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span><span class="p">;</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <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;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">14</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"##contig=<ID="</span><span class="p">))</span> <span class="p">{</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">contig_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]);</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">contig_name_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">contig_name_start</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">14</span><span class="p">));</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <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;">contig_name_end</span><span class="p">)</span> <span class="p">{</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if this line is technically well-formed (ends in '>'), it's</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// useless anyway, throw it out</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <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;">chr_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetChrCodeCounted</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">contig_name_start</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name_start</span><span class="p">);</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IsI32Neg</span><span class="p">(</span><span class="n" style="color: #333;">chr_idx</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;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">)))</span> <span class="p">{</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <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;">chr_fo_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_idx_to_foidx</span><span class="p">[</span><span class="n" style="color: #333;">chr_idx</span><span class="p">];</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">written_contig_header_lines</span><span class="p">,</span> <span class="n" style="color: #333;">chr_fo_idx</span><span class="p">)))</span> <span class="p">{</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Duplicate ##contig line in .pvar file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="p">}</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">chr_fo_idx</span><span class="p">,</span> <span class="n" style="color: #333;">written_contig_header_lines</span><span class="p">);</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if --output-chr was used at some point, we need to sync the</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ##contig chromosome code with the code in the .pvar body.</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name_write_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##contig=<ID="</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="441" 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">
441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name_write_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrtoa</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">,</span> <span class="n" style="color: #333;">chr_name_write_start</span><span class="p">);</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <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;">chr_name_write_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">chr_name_write_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">chr_name_write_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])))</span> <span class="p">{</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr 0 special case</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// note that cswritep has *not* been advanced</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">contig_zero_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// technically we write this a bit later</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="p">}</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chr_name_write_end</span><span class="p">;</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">Cswrite</span><span class="p">(</span><span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">contig_name_end</span><span class="p">,</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">contig_name_end</span><span class="p">,</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="p">}</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <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;">write_filter</span><span class="p">)</span> <span class="p">{</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FILTER=<ID="</span><span class="p">))</span> <span class="p">{</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="p">}</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <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;">write_info</span><span class="p">)</span> <span class="p">{</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID="</span><span class="p">))</span> <span class="p">{</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="p">}</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="p">}</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in the missing ##contig lines</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">contig_zero_written</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="473" 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">
473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##contig=<ID=0,length=2147483645>"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="475" 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">
475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <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;">chr_fo_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;">chr_fo_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">chr_fo_idx</span><span class="p">)</span> <span class="p">{</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">written_contig_header_lines</span><span class="p">,</span> <span class="n" style="color: #333;">chr_fo_idx</span><span class="p">))</span> <span class="p">{</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="p">}</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <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;">chr_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_file_order</span><span class="p">[</span><span class="n" style="color: #333;">chr_fo_idx</span><span class="p">];</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// AllBitsAreZero() doesn't do what we want in the --sort-vars case,</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// but fortunately we don't need it there.</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <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;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">variant_include</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">AllBitsAreZero</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chr_fo_idx</span><span class="p">],</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chr_fo_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">])))</span> <span class="p">{</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="p">}</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name_write_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##contig=<ID="</span><span class="p">);</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name_write_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrtoa</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">chr_idx</span><span class="p">,</span> <span class="n" style="color: #333;">chr_name_write_start</span><span class="p">);</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <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;">chr_name_write_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">chr_name_write_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">chr_name_write_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])))</span> <span class="p">{</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr 0 special case</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">contig_zero_written</span><span class="p">)</span> <span class="p">{</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="p">}</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">contig_zero_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">chr_name_write_end</span><span class="p">,</span> <span class="s" style="color: #d14;">",length=2147483645"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="494" 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">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">chr_name_write_end</span><span class="p">,</span> <span class="s" style="color: #d14;">",length="</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <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;">pos_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ChrLenLbound</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">,</span> <span class="n" style="color: #333;">chr_fo_idx</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">);</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">u32toa</span><span class="p">(</span><span class="n" style="color: #333;">pos_end</span><span class="p">,</span> <span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="p">}</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">;</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">AppendBinaryEoln</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="501" 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">
501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">Cswrite</span><span class="p">(</span><span class="n" style="color: #333;">css_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PvarXheaderWrite_ret_WRITE_FAIL</span><span class="p">;</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="p">}</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="p">}</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cswritep</span><span class="p">;</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="p">}</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">append_info_pr_header_line</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="508" 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">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritepp</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=PR,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Provisional reference allele, may not be based on real reference genome</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="p">}</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="p">}</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="nl">PvarXheaderWrite_ret_NOMEM:</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="nl">PvarXheaderWrite_ret_WRITE_FAIL:</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetWriteFail</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="nl">PvarXheaderWrite_ret_MALFORMED_INPUT:</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackReset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_mark</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvar</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_presents</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">),</span> <span class="k" style="font-weight: 600;">const</span> <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;">qual_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">filter_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">filter_npass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filter_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">nonref_flags</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFlags</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nonref_flags_storage</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="n" style="color: #333;">UnsortedVar</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">,</span> <span class="n" style="color: #333;">PvarPsamFlags</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">thread_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// allele_presents must be nullptr unless we're trimming alt alleles</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// split/join cases handled by WritePvarSplit() and WritePvarJoin()</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(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">@@ -316,37 +573,10 @@ PglErr WritePvar(const char* outname, const char* xheader, const uintptr_t* vari</td>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_line_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_idx</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;">// could save this during first load instead</span></span>
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<td class="diff-line-num old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
318
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"> <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;">info_pr_flag_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">info_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfInfoPrFlagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">)</span> <span class="p">{</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">write_info</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvar_ret_WRITE_FAIL</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="p">}</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Filter out FILTER/INFO definitions iff the corresponding column has</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// been removed.</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xheader</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="328" 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">
328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">[</span><span class="n" style="color: #333;">xheader_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="329" 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">
329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xheader</span><span class="p">;</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_end</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="330" 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">
330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">next_line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="331" 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">
331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <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;">write_filter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FILTER=<ID="</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num old old_line" data-linenumber="332" 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">
332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">write_info</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">StrStartsWithUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">xheader_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID="</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="333" 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">
333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_iter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="334" 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">
334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="335" 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">
335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvar_ret_WRITE_FAIL</span><span class="p">;</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="p">}</span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="p">}</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_line_start</span><span class="p">;</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp"> <span class="p">}</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">xheader_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_line_start</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="p">}</span></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">copy_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">xheader_end</span><span class="p">)</span> <span class="p">{</span></span>
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343
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<td class="diff-line-num new_line old" data-linenumber="576" 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="LC343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">copy_start</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvar_ret_WRITE_FAIL</span><span class="p">;</span></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="p">}</span></span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="348" 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">
348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="349" 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">
349
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<td class="diff-line-num new_line old" data-linenumber="576" 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="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=PR,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Provisional reference allele, may not be based on real reference genome</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="576" 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">
576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfPvarColXheader</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColVcfheader</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="350" 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="577" 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">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PvarXheaderWrite</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPvarColVcfheader</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;">write_filter</span><span class="p">,</span> <span class="n" style="color: #333;">write_info</span><span class="p">,</span> <span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">),</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">,</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="578" 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">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="579" 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">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvar_ret_1</span><span class="p">;</span></span>
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350
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<td class="diff-line-num new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
351
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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"> <span class="p">}</span></span>
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352
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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (30 Jul 2017): may be necessary to reload INFO when no ## lines</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2816" style="width: 35px; color: rgba(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">@@ -2586,7 +2816,7 @@ uintptr_t InitWriteAlleleIdxOffsets(const uintptr_t* variant_include, const uint</td>
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2586
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2816
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<pre style="margin: 0;"> <span id="LC2816" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is printed if INFO:END isn't defined, and an error occurs if either REF</span></span>
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2587
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<td class="diff-line-num new_line" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2817
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<pre style="margin: 0;"> <span id="LC2817" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is multi-character, or there's an INFO:END mismatch.</span></span>
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2588
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<td class="diff-line-num new_line" data-linenumber="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2818
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<pre style="margin: 0;"> <span id="LC2818" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Error out if REF alleles aren't all consistent, or any ALT allele is</span></span>
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2589
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<td class="diff-line-num new_line old" data-linenumber="2819" 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="LC2589" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// duplicated (n<span class="idiff left right">ecessary to use --pmerge to merge</span> the latter).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2819" 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">
2819
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<pre style="margin: 0;">+<span id="LC2819" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// duplicated (n<span class="idiff left right">ote that --pmerge must support</span> the latter).</span></span>
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2590
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<td class="diff-line-num new_line" data-linenumber="2820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2820
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<pre style="margin: 0;"> <span id="LC2820" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - For joined not-entirely-SNP non-symbolic variants, the final REF is the</span></span>
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2591
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<td class="diff-line-num new_line" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2821
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<pre style="margin: 0;"> <span id="LC2821" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// longest of the original REFs; ALT alleles have bases added to the end if</span></span>
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2592
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2822
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<pre style="margin: 0;"> <span id="LC2822" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// necessary. (Yes, this causes SNPs to stop being visible to a strlen ==</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2675" style="width: 35px; color: rgba(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="2905" style="width: 35px; color: rgba(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">@@ -2675,9 +2905,10 @@ typedef struct JoinCountsStruct {</td>
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2675
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2905
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<pre style="margin: 0;"> <span id="LC2905" class="line" lang="cpp"><span class="n" style="color: #333;">JoinVtype</span> <span class="n" style="color: #333;">JoinCount</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_alleles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">,</span> <span class="n" style="color: #333;">JoinCounts</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">jcp</span><span class="p">)</span> <span class="p">{</span></span>
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2676
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2906
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<pre style="margin: 0;"> <span id="LC2906" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">snp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2677
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2907
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<pre style="margin: 0;"> <span id="LC2907" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">symbolic_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2908
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<pre style="margin: 0;">+<span id="LC2908" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missalt_snp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2909" 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">
2909
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<pre style="margin: 0;">+<span id="LC2909" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missalt_nonsnp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2678
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<td class="diff-line-num new_line" data-linenumber="2910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2910
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<pre style="margin: 0;"> <span id="LC2910" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_alleles</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="p">{</span></span>
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2679
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<td class="diff-line-num new_line" data-linenumber="2911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2911
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<pre style="margin: 0;"> <span id="LC2911" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nonsnp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2680
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<td class="diff-line-num new_line old" data-linenumber="2912" 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="LC2680" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missalt_nonsnp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2681
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2912
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<pre style="margin: 0;"> <span id="LC2912" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">allele_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">allele_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">allele_idx</span><span class="p">)</span> <span class="p">{</span></span>
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2682
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2913
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<pre style="margin: 0;"> <span id="LC2913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_alleles</span><span class="p">[</span><span class="n" style="color: #333;">allele_idx</span><span class="p">];</span></span>
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2683
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2914
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<pre style="margin: 0;"> <span id="LC2914" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_allele</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 class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2703" style="width: 35px; color: rgba(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="2934" style="width: 35px; color: rgba(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">@@ -2703,12 +2934,12 @@ JoinVtype JoinCount(const char* const* cur_alleles, uintptr_t allele_ct, JoinCou</td>
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2703
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2934
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<pre style="margin: 0;"> <span id="LC2934" class="line" lang="cpp"> <span class="p">}</span></span>
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2704
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<td class="diff-line-num new_line" data-linenumber="2935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2935
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<pre style="margin: 0;"> <span id="LC2935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kJoinVtypeSnp</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2705
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<td class="diff-line-num new_line" data-linenumber="2936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2936
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang="cpp"> <span class="p">}</span></span>
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2706
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<pre style="margin: 0;">-<span id="LC2706" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missalt_snp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2707
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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="cpp"> <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;">allele_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">allele_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">allele_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2708
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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="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_alleles</span><span class="p">[</span><span class="n" style="color: #333;">allele_idx</span><span class="p">];</span></span>
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2709
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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="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_allele</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 class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2710
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2940
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<pre style="margin: 0;"> <span id="LC2940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kJoinVtypeError</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2711" 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">
2711
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC2711" class="line" lang="cpp"> <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;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="p">{</span></span>
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2941
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<pre style="margin: 0;">+<span id="LC2941" class="line" lang="cpp"> <span class="p">}</span></span>
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<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">
2942
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<pre style="margin: 0;">+<span id="LC2942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="p">{</span></span>
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2712
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2943
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<pre style="margin: 0;"> <span id="LC2943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2713
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2944
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<pre style="margin: 0;"> <span id="LC2944" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nonsnp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2714
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2945
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<pre style="margin: 0;"> <span id="LC2945" class="line" lang="cpp"> <span class="n" style="color: #333;">jcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">missalt_nonsnp_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3336" style="width: 35px; color: rgba(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="3567" style="width: 35px; color: rgba(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">@@ -3336,7 +3567,7 @@ PglErr ParseInfoHeader(const char* xheader, uintptr_t xheader_blen, const char*</td>
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3336
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3567
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<pre style="margin: 0;"> <span id="LC3567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
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3337
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3568
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<pre style="margin: 0;"> <span id="LC3568" class="line" lang="cpp"><span class="p">}</span></span>
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3338
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3569
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<pre style="margin: 0;"> <span id="LC3569" class="line" lang="cpp"></span>
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3339
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<pre style="margin: 0;">-<span id="LC3339" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvarSplit</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">info_keys</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">info_keys_htable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_key_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">thread_ct</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3570" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvarSplit</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">info_keys</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">info_keys_htable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">UnsortedVar</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_key_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">)</span> <span class="p">{</span></span>
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3340
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3571
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<pre style="margin: 0;"> <span id="LC3571" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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3341
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3572
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<pre style="margin: 0;"> <span id="LC3572" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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3342
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3573
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<pre style="margin: 0;"> <span id="LC3573" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3638" style="width: 35px; color: rgba(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">@@ -3407,14 +3638,18 @@ PglErr WritePvarSplit(const char* outname, const char* xheader, const uintptr_t*</td>
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3407
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3638
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<pre style="margin: 0;"> <span id="LC3638" class="line" lang="cpp"> <span class="p">}</span></span>
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3408
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<td class="diff-line-num new_line" data-linenumber="3639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3639
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<pre style="margin: 0;"> <span id="LC3639" class="line" lang="cpp"></span>
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3409
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<td class="diff-line-num new_line" data-linenumber="3640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3640
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<pre style="margin: 0;"> <span id="LC3640" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_line_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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3641
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<pre style="margin: 0;">+<span id="LC3641" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_filter</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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3642
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<pre style="margin: 0;">+<span id="LC3642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColFilter</span><span class="p">)</span> <span class="p">{</span></span>
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3643
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<pre style="margin: 0;">+<span id="LC3643" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3644
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<pre style="margin: 0;">+<span id="LC3644" class="line" lang="cpp"> <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;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColMaybefilter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filter_present</span><span class="p">)</span> <span class="p">{</span></span>
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3645
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<pre style="margin: 0;">+<span id="LC3645" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IntersectionIsEmpty</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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3646
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<pre style="margin: 0;">+<span id="LC3646" class="line" lang="cpp"> <span class="p">}</span></span>
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3410
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3647
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<pre style="margin: 0;"> <span id="LC3647" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_idx</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;">// could save this during first load instead</span></span>
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3411
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<td class="diff-line-num new_line" data-linenumber="3648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3648
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<pre style="margin: 0;"> <span id="LC3648" class="line" lang="cpp"> <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;">info_pr_flag_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">info_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfInfoPrFlagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3412
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3413" 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">
3413
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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3414
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_WRITE_FAIL</span><span class="p">;</span></span>
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3415
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3415" class="line" lang="cpp"> <span class="p">}</span></span>
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3416
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3417" 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">
3417
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<td class="diff-line-num new_line old" data-linenumber="3649" 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="LC3417" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=PR,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Provisional reference allele, may not be based on real reference genome</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3418" 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="3649" 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">
3649
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<pre style="margin: 0;">+<span id="LC3649" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfPvarColXheader</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColVcfheader</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3418" 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="3650" 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">
3650
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<pre style="margin: 0;">+<span id="LC3650" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PvarXheaderWrite</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPvarColVcfheader</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;">write_filter</span><span class="p">,</span> <span class="n" style="color: #333;">write_info</span><span class="p">,</span> <span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">),</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">,</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3651" 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">
3651
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<pre style="margin: 0;">+<span id="LC3651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3652" 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">
3652
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<pre style="margin: 0;">+<span id="LC3652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_1</span><span class="p">;</span></span>
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3418
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3653
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<pre style="margin: 0;"> <span id="LC3653" class="line" lang="cpp"> <span class="p">}</span></span>
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3419
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3654
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<pre style="margin: 0;"> <span id="LC3654" class="line" lang="cpp"> <span class="p">}</span></span>
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3420
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<td class="diff-line-num new_line" data-linenumber="3655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3655
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<pre style="margin: 0;"> <span id="LC3655" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// could also make this an array-of-structs</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3451" style="width: 35px; color: rgba(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="3686" style="width: 35px; color: rgba(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">@@ -3451,17 +3686,9 @@ PglErr WritePvarSplit(const char* outname, const char* xheader, const uintptr_t*</td>
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3451
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3686
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<pre style="margin: 0;"> <span id="LC3686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_qual</span><span class="p">)</span> <span class="p">{</span></span>
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3452
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<td class="diff-line-num new_line" data-linenumber="3687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3687
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<pre style="margin: 0;"> <span id="LC3687" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL"</span><span class="p">);</span></span>
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3453
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3688
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<pre style="margin: 0;"> <span id="LC3688" class="line" lang="cpp"> <span class="p">}</span></span>
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3454
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<td class="diff-line-num new_line old" data-linenumber="3689" 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="LC3454" class="line" lang="cpp"></span>
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3455
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<pre style="margin: 0;">-<span id="LC3455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_filter</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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3456
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<pre style="margin: 0;">-<span id="LC3456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColFilter</span><span class="p">)</span> <span class="p">{</span></span>
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3457
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<td class="diff-line-num new_line old" data-linenumber="3689" 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="LC3457" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3458
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<td class="diff-line-num new_line old" data-linenumber="3689" 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="LC3458" class="line" lang="cpp"> <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;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColMaybefilter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filter_present</span><span class="p">)</span> <span class="p">{</span></span>
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3459
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<td class="diff-line-num new_line old" data-linenumber="3689" 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="LC3459" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IntersectionIsEmpty</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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3460
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<pre style="margin: 0;">-<span id="LC3460" class="line" lang="cpp"> <span class="p">}</span></span>
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3461
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3689
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<pre style="margin: 0;"> <span id="LC3689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_filter</span><span class="p">)</span> <span class="p">{</span></span>
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3462
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3690
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<pre style="margin: 0;"> <span id="LC3690" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILTER"</span><span class="p">);</span></span>
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3463
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3691
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<pre style="margin: 0;"> <span id="LC3691" class="line" lang="cpp"> <span class="p">}</span></span>
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3464
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<td class="diff-line-num new_line old" data-linenumber="3692" 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="LC3464" class="line" lang="cpp"></span>
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3465
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3692
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<pre style="margin: 0;"> <span id="LC3692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_info</span><span class="p">)</span> <span class="p">{</span></span>
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3466
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3693
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<pre style="margin: 0;"> <span id="LC3693" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">INFO"</span><span class="p">);</span></span>
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3467
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3694
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<pre style="margin: 0;"> <span id="LC3694" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3986" style="width: 35px; color: rgba(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="4213" style="width: 35px; color: rgba(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">@@ -3986,7 +4213,7 @@ PglErr MakeFilterHtable(const uintptr_t* variant_include, const uintptr_t* filte</td>
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3986
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4213
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<pre style="margin: 0;"> <span id="LC4213" class="line" lang="cpp"><span class="p">}</span></span>
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3987
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4214
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<pre style="margin: 0;"> <span id="LC4214" class="line" lang="cpp"></span>
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3988
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4215
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<pre style="margin: 0;"> <span id="LC4215" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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3989
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<td class="diff-line-num new_line old" data-linenumber="4216" 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="LC3989" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">PglErr WritePvarJoin(const char* outname, const <span class="idiff left right">char* xheader, const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bps, const char* const* variant_ids, const uintptr_t* allele_idx_offsets, const char* const* allele_storage, const uintptr_t* qual_present, const float* quals, const uintptr_t* filter_present, const uintptr_t* filter_npass, const char* const* filter_storage, const uintptr_t* nonref_flags, const char* pvar_info_reload, const double* variant_cms, const char* varid_template_str, const char* missing_varid_match, const char* const* info_keys, const uint32_t* info_keys_htable, uint32_t raw_variant_ct, uint32_t variant_ct, uint32_t max_allele_slen, uint32_t new_variant_id_max_allele_slen, uint32_t max_write_allele_ct, uint32_t max_missalt_ct, uintptr_t xheader_blen, InfoFlags info_flags, uint32_t nonref_flags_storage, uint32_t max_filter_slen, uint32_t info_reload_slen, uint32_t info_key_ct, uint32_t info_keys_htable_size, MiscFlags misc_flags, MakePlink2Flags make_plink2_flags, PvarPsamFlags pvar_psam_flags, uint32_t thread_ct</span>) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3990" 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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4216
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<pre style="margin: 0;">+<span id="LC4216" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">PglErr WritePvarJoin(const char* outname, const <span class="idiff left right">uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bps, const char* const* variant_ids, const uintptr_t* allele_idx_offsets, const char* const* allele_storage, const uintptr_t* qual_present, const float* quals, const uintptr_t* filter_present, const uintptr_t* filter_npass, const char* const* filter_storage, const uintptr_t* nonref_flags, const char* pvar_info_reload, const double* variant_cms, const char* varid_template_str, const char* missing_varid_match, const char* const* info_keys, const uint32_t* info_keys_htable, uint32_t raw_variant_ct, uint32_t variant_ct, uint32_t max_allele_slen, uint32_t new_variant_id_max_allele_slen, uint32_t max_write_allele_ct, uint32_t max_missalt_ct, uintptr_t xheader_blen, InfoFlags info_flags, uint32_t nonref_flags_storage, uint32_t max_filter_slen, uint32_t info_reload_slen, UnsortedVar vpos_sortstatus, uint32_t info_key_ct, uint32_t info_keys_htable_size, MiscFlags misc_flags, MakePlink2Flags make_plink2_flags, PvarPsamFlags pvar_psam_flags, uint32_t thread_ct, char* xheader</span>) {</span></span>
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3990
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4217
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<pre style="margin: 0;"> <span id="LC4217" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> unsigned char* bigstack_mark = g_bigstack_base;</span></span>
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3991
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<td class="diff-line-num new_line" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4218
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<pre style="margin: 0;"> <span id="LC4218" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> char* cswritep = nullptr;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3992
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<td class="diff-line-num new_line" data-linenumber="4219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4219
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4219" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> PglErr reterr = kPglRetSuccess;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4057" style="width: 35px; color: rgba(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="4284" style="width: 35px; color: rgba(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">@@ -4057,14 +4284,18 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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<td class="diff-line-num old_line" data-linenumber="4057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4057
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<td class="diff-line-num new_line" data-linenumber="4284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4284
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<pre style="margin: 0;"> <span id="LC4284" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4058
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<td class="diff-line-num new_line" data-linenumber="4285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4285
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4285" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4059
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<td class="diff-line-num new_line" data-linenumber="4286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4286
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4286" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> char* pvar_info_line_iter = nullptr;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4287" 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">
4287
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<pre style="margin: 0;">+<span id="LC4287" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t write_filter = 0;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4288" 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">
4288
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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="LC4288" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_psam_flags & kfPvarColFilter) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4289" 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">
4289
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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="LC4289" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_filter = 1;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4290" 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">
4290
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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="LC4290" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else if ((pvar_psam_flags & kfPvarColMaybefilter) && filter_present) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4291" 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">
4291
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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="LC4291" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_filter = !IntersectionIsEmpty(variant_include, filter_present, raw_variant_ctl);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4060" 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="4292" 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">
4292
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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="LC4292" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4060
</td>
<td class="diff-line-num new_line" data-linenumber="4293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4293
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4293" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t info_col_idx = 0; // could save this during first load instead</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4061
</td>
<td class="diff-line-num new_line" data-linenumber="4294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4294
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4294" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t info_pr_flag_present = (info_flags / kfInfoPrFlagPresent) & 1;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4062" 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">
4062
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4062" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_psam_flags & kfPvarColXheader) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4063" 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">
4063
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4063" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(CsputsStd(xheader, xheader_blen, &css, &cswritep))) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4064" 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">
4064
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4064" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_WRITE_FAIL;</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="4065" 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">
4065
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4065" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</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="4066" 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">
4066
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4066" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_info_pr && (!info_pr_flag_present)) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4067" 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">
4067
</td>
<td class="diff-line-num new_line old" data-linenumber="4295" 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="LC4067" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya_k(cswritep, "##INFO=<ID=PR,Number=0,Type=Flag,Description=\"Provisional reference allele, may not be based on real reference genome\">" EOLN_STR);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4068" 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="4295" 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">
4295
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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="LC4295" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_psam_flags & (kfPvarColXheader | kfPvarColVcfheader)) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4068" 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="4296" 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">
4296
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4296" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = PvarXheaderWrite(variant_include, cip, variant_bps, allele_idx_offsets, allele_storage, nullptr, xheader_blen, (pvar_psam_flags / kfPvarColVcfheader) & 1, write_filter, write_info, write_info_pr && (!info_pr_flag_present), max_allele_slen, vpos_sortstatus, xheader, &css, &cswritep);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4068" 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="4297" 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">
4297
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4297" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(reterr)) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4068" 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="4298" 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">
4298
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4298" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_1;</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="4068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4068
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4299
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<pre style="margin: 0;"> <span id="LC4299" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old_line" data-linenumber="4069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4069
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<td class="diff-line-num new_line" data-linenumber="4300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4300
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<pre style="margin: 0;"> <span id="LC4300" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old_line" data-linenumber="4070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4070
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<td class="diff-line-num new_line" data-linenumber="4301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4301
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<pre style="margin: 0;"> <span id="LC4301" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t join_mode = (make_plink2_flags & (kfMakePlink2MSplitBase * 7));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4092" style="width: 35px; color: rgba(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="4323" style="width: 35px; color: rgba(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">@@ -4092,13 +4323,6 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4092
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<td class="diff-line-num new_line" data-linenumber="4323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4323
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<pre style="margin: 0;"> <span id="LC4323" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_qual) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4093
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<td class="diff-line-num new_line" data-linenumber="4324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4324
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<pre style="margin: 0;"> <span id="LC4324" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya_k(cswritep, "\tQUAL");</span></span>
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<td class="diff-line-num old_line" data-linenumber="4094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4094
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<td class="diff-line-num new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4325
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<pre style="margin: 0;"> <span id="LC4325" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4095
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4095" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="4096" 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">
4096
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4096" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t write_filter = 0;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4097" 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">
4097
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4097" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_psam_flags & kfPvarColFilter) {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4098" 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">
4098
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4098" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_filter = 1;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4099" 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">
4099
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4099" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else if ((pvar_psam_flags & kfPvarColMaybefilter) && filter_present) {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4100" 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">
4100
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4100" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_filter = !IntersectionIsEmpty(variant_include, filter_present, raw_variant_ctl);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4101" 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">
4101
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<td class="diff-line-num new_line old" data-linenumber="4326" 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="LC4101" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old_line" data-linenumber="4102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4102
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<td class="diff-line-num new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4326
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<pre style="margin: 0;"> <span id="LC4326" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char** filter_keys = nullptr;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4103
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<td class="diff-line-num new_line" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4327
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<pre style="margin: 0;"> <span id="LC4327" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t* filter_keys_htable = nullptr;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4104
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<td class="diff-line-num new_line" data-linenumber="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4328
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<pre style="margin: 0;"> <span id="LC4328" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uintptr_t* cur_filter_keys = nullptr;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4127" style="width: 35px; color: rgba(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="4351" style="width: 35px; color: rgba(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">@@ -4127,8 +4351,9 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4127
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4351
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<pre style="margin: 0;"> <span id="LC4351" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="4128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4128
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<td class="diff-line-num new_line" data-linenumber="4352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4352
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<pre style="margin: 0;"> <span id="LC4352" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> char** info_bufs = nullptr;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4129
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<td class="diff-line-num new_line" data-linenumber="4353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4353
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<pre style="margin: 0;"> <span id="LC4353" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char** info_starts = nullptr;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4130" 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">
4130
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<td class="diff-line-num new_line old" data-linenumber="4354" 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="LC4130" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char** info_ends = nullptr;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4131" 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="4354" 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">
4354
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<pre style="margin: 0;">+<span id="LC4354" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char** info_ends = nullptr;<span class="idiff left right"> // ugh, this is not related to INFO:END</span></span></span>
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4131
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<td class="diff-line-num new_line" data-linenumber="4355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4355
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<pre style="margin: 0;"> <span id="LC4355" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char** info_curs = nullptr;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4132" 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="4356" 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">
4356
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<pre style="margin: 0;">+<span id="LC4356" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t info_end_key_idx = UINT32_MAX;</span></span>
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4132
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4357
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<pre style="margin: 0;"> <span id="LC4357" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_info_reload) {</span></span>
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4133
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<td class="diff-line-num new_line" data-linenumber="4358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4358
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<pre style="margin: 0;"> <span id="LC4358" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(</span></span>
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4134
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4359
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<pre style="margin: 0;"> <span id="LC4359" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bigstack_alloc_cp(info_cache_size, &info_bufs) ||</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4141" style="width: 35px; color: rgba(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="4366" style="width: 35px; color: rgba(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">@@ -4141,6 +4366,16 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4141
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<td class="diff-line-num new_line" data-linenumber="4366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4366
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<pre style="margin: 0;"> <span id="LC4366" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(reterr)) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4142
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<td class="diff-line-num new_line" data-linenumber="4367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4367
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<pre style="margin: 0;"> <span id="LC4367" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_TSTREAM_FAIL;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4143
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<td class="diff-line-num new_line" data-linenumber="4368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4368
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<pre style="margin: 0;"> <span id="LC4368" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4369" 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">
4369
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<pre style="margin: 0;">+<span id="LC4369" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> info_end_key_idx = IdHtableFind("END", info_keys, info_keys_htable, strlen("END"), info_keys_htable_size);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4370" 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">
4370
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<pre style="margin: 0;">+<span id="LC4370" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (info_end_key_idx != UINT32_MAX) {</span></span>
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4371
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<pre style="margin: 0;">+<span id="LC4371" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const int32_t knum = const_container_of[info_keys[info_end_key_idx], InfoVtype, key)->num;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4372" 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">
4372
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<pre style="margin: 0;">+<span id="LC4372" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((knum != 1) && (knum != kInfoVtypeUnknown)) {</span></span>
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4373
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<pre style="margin: 0;">+<span id="LC4373" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO: verify type instead.</span></span>
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4374
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<pre style="margin: 0;">+<span id="LC4374" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // but if number is not . or 1, this is not the INFO:END we're</span></span>
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4375
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<pre style="margin: 0;">+<span id="LC4375" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // looking for.</span></span>
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4376
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<pre style="margin: 0;">+<span id="LC4376" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> info_end_key_idx = UINT32_MAX;</span></span>
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4377
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<pre style="margin: 0;">+<span id="LC4377" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4378
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<pre style="margin: 0;">+<span id="LC4378" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4144
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4379
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<pre style="margin: 0;"> <span id="LC4379" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4145
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<td class="diff-line-num new_line" data-linenumber="4380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4380
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<pre style="margin: 0;"> <span id="LC4380" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_info) {</span></span>
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4146
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<td class="diff-line-num new_line" data-linenumber="4381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4381
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<pre style="margin: 0;"> <span id="LC4381" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya_k(cswritep, "\tINFO");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4192" style="width: 35px; color: rgba(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="4427" style="width: 35px; color: rgba(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">@@ -4192,13 +4427,12 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4192
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<td class="diff-line-num new_line" data-linenumber="4427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4427
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<pre style="margin: 0;"> <span id="LC4427" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t pct = 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4193
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<td class="diff-line-num new_line" data-linenumber="4428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4428
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<pre style="margin: 0;"> <span id="LC4428" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t next_print_variant_idx = variant_ct / 100;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4194
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<td class="diff-line-num new_line" data-linenumber="4429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4429
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<pre style="margin: 0;"> <span id="LC4429" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> JoinCounts jc;</span></span>
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4195
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<pre style="margin: 0;">-<span id="LC4195" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> JoinCounts next_jc;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4196
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<td class="diff-line-num new_line" data-linenumber="4430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4430
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<pre style="margin: 0;"> <span id="LC4430" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.snp_ct = 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4197
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<td class="diff-line-num new_line" data-linenumber="4431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4431
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<pre style="margin: 0;"> <span id="LC4431" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.nonsnp_ct = 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4198
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<td class="diff-line-num new_line" data-linenumber="4432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4432
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<pre style="margin: 0;"> <span id="LC4432" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.symbolic_ct = 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4199
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<td class="diff-line-num new_line" data-linenumber="4433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4433
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<pre style="margin: 0;"> <span id="LC4433" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.missalt_snp_ct = 0;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4200
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<td class="diff-line-num new_line" data-linenumber="4434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4434
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<pre style="margin: 0;"> <span id="LC4434" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.missalt_nonsnp_ct = 0;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4201" 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">
4201
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<td class="diff-line-num new_line old" data-linenumber="4435" 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="LC4201" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">;;</span>;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4202" 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="4435" 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">
4435
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<pre style="margin: 0;">+<span id="LC4435" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">JoinCounts next_jc = jc</span>;</span></span>
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4202
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<td class="diff-line-num new_line" data-linenumber="4436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4436
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<pre style="margin: 0;"> <span id="LC4436" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fputs("0%", stdout);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4203
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<td class="diff-line-num new_line" data-linenumber="4437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4437
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<pre style="margin: 0;"> <span id="LC4437" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fflush(stdout);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4204
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<td class="diff-line-num new_line" data-linenumber="4438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4438
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<pre style="margin: 0;"> <span id="LC4438" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> while (1) {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4232" style="width: 35px; color: rgba(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="4466" style="width: 35px; color: rgba(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">@@ -4232,6 +4466,12 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4232
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<td class="diff-line-num new_line" data-linenumber="4466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4466
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<pre style="margin: 0;"> <span id="LC4466" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> allele_ct = allele_idx_offsets[next_variant_uidx + 1] - allele_idx_offset_base;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4233
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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="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old_line" data-linenumber="4234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4234
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<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="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* const* cur_alleles = &(allele_storage[allele_idx_offset_base]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4469" 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">
4469
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<pre style="margin: 0;">+<span id="LC4469" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> JoinVtype jvt = JoinCount(cur_alleles, allele_ct, &next_jc);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4470" 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">
4470
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<pre style="margin: 0;">+<span id="LC4470" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // previously validated</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4471" 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">
4471
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<pre style="margin: 0;">+<span id="LC4471" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((join_mode == kfMakePlink2MJoinSnps) && ) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4472" 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">
4472
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<pre style="margin: 0;">+<span id="LC4472" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4473
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<pre style="margin: 0;">+<span id="LC4473" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="4474" 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">
4474
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<pre style="margin: 0;">+<span id="LC4474" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO</span></span>
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4235
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<td class="diff-line-num new_line" data-linenumber="4475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4475
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<pre style="margin: 0;"> <span id="LC4475" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.snp_ct += next_jc.snp_ct;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4236
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<td class="diff-line-num new_line" data-linenumber="4476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4476
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<pre style="margin: 0;"> <span id="LC4476" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.nonsnp_ct += next_jc.nonsnp_ct;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4237
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<td class="diff-line-num new_line" data-linenumber="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4477
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<pre style="margin: 0;"> <span id="LC4477" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.symbolic_ct += next_jc.symbolic_ct;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4331" style="width: 35px; color: rgba(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="4571" style="width: 35px; color: rgba(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">@@ -4331,12 +4571,18 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4331
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4571
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<pre style="margin: 0;"> <span id="LC4571" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4332
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4572
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<pre style="margin: 0;"> <span id="LC4572" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> AppendBinaryEoln(&cswritep);</span></span>
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4333
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4573
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<pre style="margin: 0;"> <span id="LC4573" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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4574
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<pre style="margin: 0;">+<span id="LC4574" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO</span></span>
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4575
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<pre style="margin: 0;">+<span id="LC4575" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.snp_ct = 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4576" 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">
4576
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<pre style="margin: 0;">+<span id="LC4576" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.nonsnp_ct = 0;</span></span>
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4577
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<pre style="margin: 0;">+<span id="LC4577" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.symbolic_ct = 0;</span></span>
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4578
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<pre style="margin: 0;">+<span id="LC4578" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_snp_ct = 0;</span></span>
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4579
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<pre style="margin: 0;">+<span id="LC4579" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_nonsnp_ct = 0;</span></span>
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4334
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4580
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<pre style="margin: 0;"> <span id="LC4580" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4335
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4581
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<pre style="margin: 0;"> <span id="LC4581" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (next_variant_idx == variant_ct) {</span></span>
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4336
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4582
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<pre style="margin: 0;"> <span id="LC4582" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
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4337
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4583
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<pre style="margin: 0;"> <span id="LC4583" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4338
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4584
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<pre style="margin: 0;"> <span id="LC4584" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> this_pos_write_variant_ct = 0;</span></span>
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4339
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<pre style="margin: 0;">-<span id="LC4339" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> j<span class="idiff left right">t = next_jt</span>;</span></span>
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4585
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<pre style="margin: 0;">+<span id="LC4585" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> j<span class="idiff left right">c = next_jc</span>;</span></span>
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4340
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4586
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<pre style="margin: 0;"> <span id="LC4586" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> prev_bp = cur_bp;</span></span>
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4341
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4587
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<pre style="margin: 0;"> <span id="LC4587" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_idx = next_variant_idx;</span></span>
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4342
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4588
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<pre style="margin: 0;"> <span id="LC4588" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_uidx = next_variant_uidx;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4377" style="width: 35px; color: rgba(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="4623" style="width: 35px; color: rgba(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">@@ -4377,6 +4623,7 @@ PglErr WritePvarJoin(const char* outname, const char* xheader, const uintptr_t*</td>
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4377
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4623
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<pre style="margin: 0;"> <span id="LC4623" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4378
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4624
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<pre style="margin: 0;"> <span id="LC4624" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4379
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4625
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<pre style="margin: 0;"> <span id="LC4625" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4626
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<pre style="margin: 0;">+<span id="LC4626" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4380
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4627
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<pre style="margin: 0;"> <span id="LC4627" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4381
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4628
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<pre style="margin: 0;"> <span id="LC4628" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(CswriteCloseNull(&css, cswritep))) {</span></span>
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4382
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4629
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<pre style="margin: 0;"> <span id="LC4629" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_WRITE_FAIL;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5605" style="width: 35px; color: rgba(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="5852" style="width: 35px; color: rgba(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">@@ -5605,20 +5852,24 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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5605
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<td class="diff-line-num new_line" data-linenumber="5852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5852
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<pre style="margin: 0;"> <span id="LC5852" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (25 Jul 2018): left expression needs ||, not &&</span></span>
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5606
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<td class="diff-line-num new_line" data-linenumber="5853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5853
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<pre style="margin: 0;"> <span id="LC5853" class="line" lang="cpp"> <span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">hard_call_thresh</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</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;">read_dosage_present</span><span class="p">))</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">kDosage4th</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hard_call_thresh</span><span class="p">);</span></span>
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5607
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5854
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<pre style="margin: 0;"> <span id="LC5854" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_halfdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kDosage4th</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">;</span></span>
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5608
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<td class="diff-line-num new_line old" data-linenumber="5855" 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="LC5608" class="line" lang="cpp"> <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;">read_hphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPgenGlobalHardcallPhasePresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5855
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<pre style="margin: 0;">+<span id="LC5855" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix/simplification (10 Mar 2020): it is possible for dosage-phase</span></span>
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5856
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<pre style="margin: 0;">+<span id="LC5856" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// to be present in the input without hardcall-phase. Don't try to treat</span></span>
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5857
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<pre style="margin: 0;">+<span id="LC5857" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that differently than the usual scenario where hardcall-phase is</span></span>
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5858
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<pre style="margin: 0;">+<span id="LC5858" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// present.</span></span>
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5859
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<pre style="margin: 0;">+<span id="LC5859" class="line" lang="cpp"> <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;">read_phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!!</span><span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfPgenGlobalHardcallPhasePresent</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePhasePresent</span><span class="p">));</span></span>
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5609
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<td class="diff-line-num new_line" data-linenumber="5860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5860
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<pre style="margin: 0;"> <span id="LC5860" class="line" lang="cpp"> <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;">read_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePhasePresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5610
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5861
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<pre style="margin: 0;"> <span id="LC5861" class="line" lang="cpp"> <span class="n" style="color: #333;">PgenGlobalFlags</span> <span class="n" style="color: #333;">write_gflags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_gflags</span><span class="p">;</span></span>
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5611
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<td class="diff-line-num new_line" data-linenumber="5862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5862
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<pre style="margin: 0;"> <span id="LC5862" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// When --hard-call-threshold is specified, if either hphase or dphase</span></span>
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5612
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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">
5863
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<pre style="margin: 0;"> <span id="LC5863" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// values exist, the other can be generated.</span></span>
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5613
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<td class="diff-line-num new_line old" data-linenumber="5864" 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="LC5613" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_<span class="idiff left">hphase_present</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">read_h</span>phase_present</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5614" 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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5864
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<pre style="margin: 0;">+<span id="LC5864" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_<span class="idiff left">phase_present</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">read_</span>phase_present</span><span class="p">;</span></span>
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5614
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<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">
5865
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<pre style="margin: 0;"> <span id="LC5865" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_dphase_present</span><span class="p">;</span></span>
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5615
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<td class="diff-line-num new_line old" data-linenumber="5866" 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="LC5615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5616" 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">
5616
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<td class="diff-line-num new_line old" data-linenumber="5866" 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="LC5616" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5617" 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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5866
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<pre style="margin: 0;">+<span id="LC5866" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span><span class="p">))</span> <span class="p">{</span></span>
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<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">
5867
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<pre style="margin: 0;">+<span id="LC5867" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5617
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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="cpp"> <span class="n" style="color: #333;">read_or_write_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5618
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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="cpp"> <span class="n" style="color: #333;">write_gflags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfPgenGlobalHardcallPhasePresent</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePhasePresent</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5619
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<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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<pre style="margin: 0;"> <span id="LC5870" class="line" lang="cpp"> <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;">dosage_erase_thresh</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5620
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<td class="diff-line-num new_line" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5871
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<pre style="margin: 0;"> <span id="LC5871" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// need write_phasepresent, pretty harmless to allocate write_phaseinfo</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5621" 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">
5621
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<td class="diff-line-num new_line old" data-linenumber="5872" 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="LC5621" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5872
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<pre style="margin: 0;">+<span id="LC5872" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5622
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5873
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<pre style="margin: 0;"> <span id="LC5873" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="5623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5623
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5874
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<pre style="margin: 0;"> <span id="LC5874" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5624
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<td class="diff-line-num new_line" data-linenumber="5875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5875
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<pre style="margin: 0;"> <span id="LC5875" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plink2_write_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPlink2WriteLateDosageErase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5708" style="width: 35px; color: rgba(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="5959" style="width: 35px; color: rgba(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">@@ -5708,7 +5959,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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5708
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<td class="diff-line-num new_line" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5959
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<pre style="margin: 0;"> <span id="LC5959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_wp</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_genovecs</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5709
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<td class="diff-line-num new_line" data-linenumber="5960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5960
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<pre style="margin: 0;"> <span id="LC5960" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePgenRobust_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5710
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<td class="diff-line-num new_line" data-linenumber="5961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5961
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<pre style="margin: 0;"> <span id="LC5961" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5711
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<td class="diff-line-num new_line old" data-linenumber="5962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5711" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5712" 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="5962" 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">
5962
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<pre style="margin: 0;">+<span id="LC5962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5712
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<td class="diff-line-num new_line" data-linenumber="5963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5963
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<pre style="margin: 0;"> <span id="LC5963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5713
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<td class="diff-line-num new_line" data-linenumber="5964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5964
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<pre style="margin: 0;"> <span id="LC5964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePgenRobust_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5714
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<td class="diff-line-num new_line" data-linenumber="5965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5965
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<pre style="margin: 0;"> <span id="LC5965" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5734" style="width: 35px; color: rgba(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="5985" style="width: 35px; color: rgba(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">@@ -5734,7 +5985,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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<td class="diff-line-num old_line" data-linenumber="5734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5734
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<td class="diff-line-num new_line" data-linenumber="5985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5985
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<pre style="margin: 0;"> <span id="LC5985" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5735
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<td class="diff-line-num new_line" data-linenumber="5986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5986
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<pre style="margin: 0;"> <span id="LC5986" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phasepresents</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5736
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<td class="diff-line-num new_line" data-linenumber="5987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5987
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<pre style="margin: 0;"> <span id="LC5987" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5737" 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">
5737
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<td class="diff-line-num new_line old" data-linenumber="5988" 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="LC5737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</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="5738" 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="5988" 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">
5988
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<pre style="margin: 0;">+<span id="LC5988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5738
</td>
<td class="diff-line-num new_line" data-linenumber="5989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5989
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5739
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<td class="diff-line-num new_line" data-linenumber="5990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5990
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5990" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_wp</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phasepresents</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="5740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5740
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<td class="diff-line-num new_line" data-linenumber="5991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5991
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<pre style="margin: 0;"> <span id="LC5991" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_wp</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phaseinfos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5742" style="width: 35px; color: rgba(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="5993" style="width: 35px; color: rgba(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">@@ -5742,7 +5993,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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<td class="diff-line-num old_line" data-linenumber="5742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5742
</td>
<td class="diff-line-num new_line" data-linenumber="5993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5993
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5993" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</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="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phaseinfos</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5743
</td>
<td class="diff-line-num new_line" data-linenumber="5994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5994
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<pre style="margin: 0;"> <span id="LC5994" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePgenRobust_ret_NOMEM</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5744
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<td class="diff-line-num new_line" data-linenumber="5995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5995
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5995" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5745" 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">
5745
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<td class="diff-line-num new_line old" data-linenumber="5996" 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="LC5745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</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="5746" 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="5996" 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">
5996
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<pre style="margin: 0;">+<span id="LC5996" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5746
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<td class="diff-line-num new_line" data-linenumber="5997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5997
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5997" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="5747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5747
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<td class="diff-line-num new_line" data-linenumber="5998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5998
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5998" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_wp</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</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="5748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5748
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<td class="diff-line-num new_line" data-linenumber="5999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5999
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5999" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="5834" style="width: 35px; color: rgba(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="6085" style="width: 35px; color: rgba(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">@@ -5834,7 +6085,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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<td class="diff-line-num old_line" data-linenumber="5834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5834
</td>
<td class="diff-line-num new_line" data-linenumber="6085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6085
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<pre style="margin: 0;"> <span id="LC6085" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32p</span><span class="p">(</span><span class="n" style="color: #333;">max_read_allele_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;">alt_two_sample_idx_starts</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5835
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<td class="diff-line-num new_line" data-linenumber="6086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6086
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<pre style="margin: 0;"> <span id="LC6086" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePgenRobust_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5836
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<td class="diff-line-num new_line" data-linenumber="6087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6087
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<pre style="margin: 0;"> <span id="LC6087" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5837" 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">
5837
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<td class="diff-line-num new_line old" data-linenumber="6088" 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="LC5837" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5838" 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="6088" 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">
6088
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<pre style="margin: 0;">+<span id="LC6088" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5838
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<td class="diff-line-num new_line" data-linenumber="6089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6089
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<pre style="margin: 0;"> <span id="LC6089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="5839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5839
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<td class="diff-line-num new_line" data-linenumber="6090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6090
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<pre style="margin: 0;"> <span id="LC6090" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgv</span><span class="p">.</span><span class="n" style="color: #333;">phasepresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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5840
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<td class="diff-line-num new_line" data-linenumber="6091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6091
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<pre style="margin: 0;"> <span id="LC6091" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgv</span><span class="p">.</span><span class="n" style="color: #333;">phaseinfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5853" style="width: 35px; color: rgba(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="6104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5853,9 +6104,9 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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5853
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<td class="diff-line-num new_line" data-linenumber="6104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6104
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<pre style="margin: 0;"> <span id="LC6104" class="line" lang="cpp"> <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;">raw_sample_ctv2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NypCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="5854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5854
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<td class="diff-line-num new_line" data-linenumber="6105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6105
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<pre style="margin: 0;"> <span id="LC6105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">load_variant_vec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_sample_ctv2</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5855
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<td class="diff-line-num new_line" data-linenumber="6106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6106
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<pre style="margin: 0;"> <span id="LC6106" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loaded_vrtypes_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalMultiallelicHardcallFound</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5856
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<td class="diff-line-num new_line old" data-linenumber="6107" 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="LC5856" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6107" 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">
6107
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<pre style="margin: 0;">+<span id="LC6107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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5857
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<td class="diff-line-num new_line" data-linenumber="6108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6108
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<pre style="margin: 0;"> <span id="LC6108" class="line" lang="cpp"> <span class="n" style="color: #333;">loaded_vrtypes_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5858
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<td class="diff-line-num new_line old" data-linenumber="6109" 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="LC5858" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6109
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<pre style="margin: 0;">+<span id="LC6109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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5859
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<td class="diff-line-num new_line" data-linenumber="6110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6110
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<pre style="margin: 0;"> <span id="LC6110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// phaseraw has three parts:</span></span>
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5860
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<td class="diff-line-num new_line" data-linenumber="6111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6111
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<pre style="margin: 0;"> <span id="LC6111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. het_ct as uint32_t, and explicit_phasepresent_ct as uint32_t.</span></span>
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<td class="diff-line-num old_line" data-linenumber="5861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5861
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<td class="diff-line-num new_line" data-linenumber="6112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6112
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<pre style="margin: 0;"> <span id="LC6112" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2. vec-aligned bitarray of up to (raw_sample_ct + 1) bits. first</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5985" style="width: 35px; color: rgba(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="6236" style="width: 35px; color: rgba(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">@@ -5985,7 +6236,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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5985
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<td class="diff-line-num new_line" data-linenumber="6236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6236
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<pre style="margin: 0;"> <span id="LC6236" class="line" lang="cpp"> <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;">cur_write_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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5986
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6237
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<pre style="margin: 0;"> <span id="LC6237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_aidx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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5987
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6238
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<pre style="margin: 0;"> <span id="LC6238" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. read into normal, not raw representation</span></span>
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5988
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<pre style="margin: 0;">-<span id="LC5988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6239
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<pre style="margin: 0;">+<span id="LC6239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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5989
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6240
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<pre style="margin: 0;"> <span id="LC6240" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PgrGetMDp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">null_pssi</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">read_variant_uidx</span><span class="p">,</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgv</span><span class="p">);</span></span>
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5990
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6241
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<pre style="margin: 0;"> <span id="LC6241" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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5991
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6242
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<pre style="margin: 0;"> <span id="LC6242" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PgrGetMD</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">null_pssi</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">read_variant_uidx</span><span class="p">,</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgv</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6395,7 +6646,7 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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6395
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6646
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<pre style="margin: 0;"> <span id="LC6646" class="line" lang="cpp"><span class="p">}</span></span>
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6396
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6647
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<pre style="margin: 0;"> <span id="LC6647" class="line" lang="cpp"></span>
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6397
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6648
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<pre style="margin: 0;"> <span id="LC6648" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// allele_presents should be nullptr iff trim_alts not true</span></span>
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6398
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<pre style="margin: 0;">-<span id="LC6398" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pgr_alloc_cacheline_ct</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6649" 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="LC6649" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">UnsortedVar</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgr_alloc_cacheline_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">)</span> <span class="p">{</span></span>
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6399
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6650
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<pre style="margin: 0;"> <span id="LC6650" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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6400
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6651
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<pre style="margin: 0;"> <span id="LC6651" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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6401
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6652
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<pre style="margin: 0;"> <span id="LC6652" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6752" style="width: 35px; color: rgba(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">@@ -6501,7 +6752,7 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6501
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6752
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<pre style="margin: 0;"> <span id="LC6752" class="line" lang="cpp"> <span class="n" style="color: #333;">nonref_flags_storage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pgfip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalAllNonref</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6502
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6753
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<pre style="margin: 0;"> <span id="LC6753" class="line" lang="cpp"> <span class="p">}</span></span>
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6503
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6754
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<pre style="margin: 0;"> <span id="LC6754" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_variant_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6504
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<pre style="margin: 0;">-<span id="LC6504" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvar</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgfip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_thread_ct</span></span><span class="p">);</span></span>
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6755
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<pre style="margin: 0;">+<span id="LC6755" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvar</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgfip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">xheader</span></span><span class="p">);</span></span>
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6505
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6756
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<pre style="margin: 0;"> <span id="LC6756" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6506
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6757
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<pre style="margin: 0;"> <span id="LC6757" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">info_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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6507
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6758
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<pre style="margin: 0;"> <span id="LC6758" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_key_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6765" style="width: 35px; color: rgba(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">@@ -6514,12 +6765,12 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6514
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6765
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<pre style="margin: 0;"> <span id="LC6765" class="line" lang="cpp"> <span class="p">}</span></span>
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6515
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6766
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<pre style="margin: 0;"> <span id="LC6766" class="line" lang="cpp"> <span class="p">}</span></span>
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6516
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6767
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<pre style="margin: 0;"> <span id="LC6767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_variant_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variant_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6517
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<pre style="margin: 0;">-<span id="LC6517" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvarSplit</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgfip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_key_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_thread_ct</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6768" 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">
6768
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<pre style="margin: 0;">+<span id="LC6768" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvarSplit</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgfip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_key_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_keys_htable_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">xheader</span></span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6518
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<td class="diff-line-num new_line" data-linenumber="6769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6769
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<pre style="margin: 0;"> <span id="LC6769" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6519
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<td class="diff-line-num new_line" data-linenumber="6770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6770
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<pre style="margin: 0;"> <span id="LC6770" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Multiallelic join is under development.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6520
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<td class="diff-line-num new_line" data-linenumber="6771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6771
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<pre style="margin: 0;"> <span id="LC6771" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6521
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<td class="diff-line-num new_line" data-linenumber="6772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6772
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<pre style="margin: 0;"> <span id="LC6772" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6522" 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">
6522
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<td class="diff-line-num new_line old" data-linenumber="6773" 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="LC6522" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reterr = WritePvarJoin(outname, <span class="idiff left right">xheader, variant_include, cip, variant_bps, variant_ids, allele_idx_offsets, allele_storage, pvar_qual_present, pvar_quals, pvar_filter_present, pvar_filter_npass, pvar_filter_storage, pgfip->nonref_flags, pvar_info_reload, variant_cms, varid_template_str, missing_varid_match, info_keys, info_keys_htable, raw_variant_ct, variant_ct, max_allele_slen, new_variant_id_max_allele_slen, max_write_allele_ct, max_missalt_ct, xheader_blen, info_flags, nonref_flags_storage, max_filter_slen, info_reload_slen, info_key_ct, info_keys_htable_size, misc_flags, make_plink2_flags, pvar_psam_flags, max_thread_ct</span>);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6523" 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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6773
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<pre style="margin: 0;">+<span id="LC6773" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reterr = WritePvarJoin(outname, <span class="idiff left right">variant_include, cip, variant_bps, variant_ids, allele_idx_offsets, allele_storage, pvar_qual_present, pvar_quals, pvar_filter_present, pvar_filter_npass, pvar_filter_storage, pgfip->nonref_flags, pvar_info_reload, variant_cms, varid_template_str, missing_varid_match, info_keys, info_keys_htable, raw_variant_ct, variant_ct, max_allele_slen, new_variant_id_max_allele_slen, max_write_allele_ct, max_missalt_ct, xheader_blen, info_flags, nonref_flags_storage, max_filter_slen, info_reload_slen, vpos_sortstatus, info_key_ct, info_keys_htable_size, misc_flags, make_plink2_flags, pvar_psam_flags, max_thread_ct, xheader</span>);</span></span>
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6523
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6774
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<pre style="margin: 0;"> <span id="LC6774" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6524
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6775
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<pre style="margin: 0;"> <span id="LC6775" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6525
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6776
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<pre style="margin: 0;"> <span id="LC6776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6620" style="width: 35px; color: rgba(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="6871" style="width: 35px; color: rgba(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">@@ -6620,17 +6871,17 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6620
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6871
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<pre style="margin: 0;"> <span id="LC6871" class="line" lang="cpp"> <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;">read_dosage_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6621
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6872
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<pre style="margin: 0;"> <span id="LC6872" class="line" lang="cpp"> <span class="n" style="color: #333;">mc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">hard_call_thresh</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</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;">read_dosage_present</span><span class="p">))</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">kDosage4th</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hard_call_thresh</span><span class="p">);</span></span>
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6622
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6873
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<pre style="margin: 0;"> <span id="LC6873" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">dosage_erase_halfdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kDosage4th</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dosage_erase_thresh</span><span class="p">;</span></span>
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6623
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<pre style="margin: 0;">-<span id="LC6623" class="line" lang="cpp"> <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;">read_<span class="idiff left">hphase_present</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">read_gflags</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">kfPgenGlobalHardcallPhasePresent</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="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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6874
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<pre style="margin: 0;">+<span id="LC6874" class="line" lang="cpp"> <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;">read_<span class="idiff left">phase_present</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="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read_gflags</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">kfPgenGlobalHardcallPhasePresent</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">kfPgenGlobalDosagePhasePresent</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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6624
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6875
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<pre style="margin: 0;"> <span id="LC6875" class="line" lang="cpp"> <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;">read_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePhasePresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6625
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6876
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<pre style="margin: 0;"> <span id="LC6876" class="line" lang="cpp"> <span class="n" style="color: #333;">PgenGlobalFlags</span> <span class="n" style="color: #333;">write_gflags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_gflags</span><span class="p">;</span></span>
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6626
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<pre style="margin: 0;">-<span id="LC6626" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_<span class="idiff left">hphase_present</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">read_h</span>phase_present</span><span class="p">;</span></span>
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6877
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<pre style="margin: 0;">+<span id="LC6877" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_<span class="idiff left">phase_present</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">read_</span>phase_present</span><span class="p">;</span></span>
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6627
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6878
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<pre style="margin: 0;"> <span id="LC6878" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_dphase_present</span><span class="p">;</span></span>
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6628
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<td class="diff-line-num new_line old" data-linenumber="6879" 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="LC6628" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span><span class="p">))</span> <span class="p">{</span></span>
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6629
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<pre style="margin: 0;">-<span id="LC6629" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6879
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<pre style="margin: 0;">+<span id="LC6879" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="p">.</span><span class="n" style="color: #333;">hard_call_halfdist</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dphase_present</span><span class="p">))</span> <span class="p">{</span></span>
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6880
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<pre style="margin: 0;">+<span id="LC6880" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6630
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6881
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<pre style="margin: 0;"> <span id="LC6881" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_dphase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6631
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6882
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<pre style="margin: 0;"> <span id="LC6882" class="line" lang="cpp"> <span class="n" style="color: #333;">write_gflags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfPgenGlobalHardcallPhasePresent</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPgenGlobalDosagePhasePresent</span><span class="p">;</span></span>
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6632
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6883
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<pre style="margin: 0;"> <span id="LC6883" class="line" lang="cpp"> <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;">dosage_erase_thresh</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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6633
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<pre style="margin: 0;">-<span id="LC6633" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6884
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<pre style="margin: 0;">+<span id="LC6884" class="line" lang="cpp"> <span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6634
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<td class="diff-line-num new_line" data-linenumber="6885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6885
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<pre style="margin: 0;"> <span id="LC6885" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6635
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<td class="diff-line-num new_line" data-linenumber="6886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6886
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<pre style="margin: 0;"> <span id="LC6886" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_dosage_present</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6636
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<td class="diff-line-num new_line" data-linenumber="6887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6887
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<pre style="margin: 0;"> <span id="LC6887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mc</span><span class="p">.</span><span class="n" style="color: #333;">plink2_write_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPlink2WriteLateDosageErase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6672" style="width: 35px; color: rgba(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="6923" style="width: 35px; color: rgba(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">@@ -6672,7 +6923,7 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6672
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<td class="diff-line-num new_line" data-linenumber="6923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6923
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<pre style="margin: 0;"> <span id="LC6923" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">mhcraw_word_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">kWordsPerVec</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">GetMhcWordCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6673
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<td class="diff-line-num new_line" data-linenumber="6924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6924
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<pre style="margin: 0;"> <span id="LC6924" class="line" lang="cpp"> <span class="n" style="color: #333;">load_vblock_cacheline_ct</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">WordCtToCachelineCtU64</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</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;">mhcraw_word_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_vblock_size</span><span class="p">);</span></span>
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6674
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<td class="diff-line-num new_line" data-linenumber="6925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6925
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<pre style="margin: 0;"> <span id="LC6925" class="line" lang="cpp"> <span class="p">}</span></span>
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6675
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<td class="diff-line-num new_line old" data-linenumber="6926" 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="LC6675" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6926
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<pre style="margin: 0;">+<span id="LC6926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6676
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<td class="diff-line-num new_line" data-linenumber="6927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6927
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<pre style="margin: 0;"> <span id="LC6927" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// could make this bound tighter when lots of unphased variants are</span></span>
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6677
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<td class="diff-line-num new_line" data-linenumber="6928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6928
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<pre style="margin: 0;"> <span id="LC6928" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mixed in among the phased variants, but this isn't nearly as</span></span>
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<td class="diff-line-num old_line" data-linenumber="6678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6678
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<td class="diff-line-num new_line" data-linenumber="6929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6929
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<pre style="margin: 0;"> <span id="LC6929" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// important as the analogous multiallelic optimization</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6801" style="width: 35px; color: rgba(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="7052" style="width: 35px; color: rgba(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">@@ -6801,7 +7052,7 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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<td class="diff-line-num old_line" data-linenumber="6801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6801
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<td class="diff-line-num new_line" data-linenumber="7052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7052
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<pre style="margin: 0;"> <span id="LC7052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_wp</span><span class="p">(</span><span class="n" style="color: #333;">calc_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_genovecs</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6802
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<td class="diff-line-num new_line" data-linenumber="7053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7053
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<pre style="margin: 0;"> <span id="LC7053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_fallback</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6803
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<td class="diff-line-num new_line" data-linenumber="7054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7054
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<pre style="margin: 0;"> <span id="LC7054" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6804" 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">
6804
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<td class="diff-line-num new_line old" data-linenumber="7055" 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="LC6804" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6805" 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="7055" 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">
7055
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<pre style="margin: 0;">+<span id="LC7055" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6805
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<td class="diff-line-num new_line" data-linenumber="7056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7056
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<pre style="margin: 0;"> <span id="LC7056" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6806
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<td class="diff-line-num new_line" data-linenumber="7057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7057
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<pre style="margin: 0;"> <span id="LC7057" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_fallback</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6807
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<td class="diff-line-num new_line" data-linenumber="7058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7058
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<pre style="margin: 0;"> <span id="LC7058" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6834" style="width: 35px; color: rgba(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="7085" style="width: 35px; color: rgba(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">@@ -6834,13 +7085,13 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6834
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<td class="diff-line-num new_line" data-linenumber="7085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7085
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<pre style="margin: 0;"> <span id="LC7085" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6835
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<td class="diff-line-num new_line" data-linenumber="7086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7086
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<pre style="margin: 0;"> <span id="LC7086" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_dosagepresents</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6836
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<td class="diff-line-num new_line" data-linenumber="7087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7087
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<pre style="margin: 0;"> <span id="LC7087" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_dphasepresents</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6837" 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">
6837
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<td class="diff-line-num new_line old" data-linenumber="7088" 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="LC6837" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6838" 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">
6838
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<td class="diff-line-num new_line old" data-linenumber="7088" 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="LC6838" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6839" 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="7088" 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">
7088
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<pre style="margin: 0;">+<span id="LC7088" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6839" 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="7089" 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">
7089
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<pre style="margin: 0;">+<span id="LC7089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6839
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<td class="diff-line-num new_line" data-linenumber="7090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7090
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<pre style="margin: 0;"> <span id="LC7090" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_wp</span><span class="p">(</span><span class="n" style="color: #333;">calc_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phasepresents</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num old_line" data-linenumber="6840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6840
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<td class="diff-line-num new_line" data-linenumber="7091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7091
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<pre style="margin: 0;"> <span id="LC7091" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_wp</span><span class="p">(</span><span class="n" style="color: #333;">calc_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phaseinfos</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6841
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<td class="diff-line-num new_line" data-linenumber="7092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7092
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<pre style="margin: 0;"> <span id="LC7092" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_fallback</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6842
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<td class="diff-line-num new_line" data-linenumber="7093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7093
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<pre style="margin: 0;"> <span id="LC7093" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6843" 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">
6843
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<td class="diff-line-num new_line old" data-linenumber="7094" 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="LC6843" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</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="6844" 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="7094" 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">
7094
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<pre style="margin: 0;">+<span id="LC7094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6844
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<td class="diff-line-num new_line" data-linenumber="7095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7095
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<pre style="margin: 0;"> <span id="LC7095" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_wp</span><span class="p">(</span><span class="n" style="color: #333;">calc_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6845
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<td class="diff-line-num new_line" data-linenumber="7096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7096
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<pre style="margin: 0;"> <span id="LC7096" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_fallback</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6846
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<td class="diff-line-num new_line" data-linenumber="7097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7097
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<pre style="margin: 0;"> <span id="LC7097" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6869" style="width: 35px; color: rgba(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="7120" style="width: 35px; color: rgba(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">@@ -6869,7 +7120,7 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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<td class="diff-line-num old_line" data-linenumber="6869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6869
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<td class="diff-line-num new_line" data-linenumber="7120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7120
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<pre style="margin: 0;"> <span id="LC7120" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// todo: multiallelic dosage</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6870
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<td class="diff-line-num new_line" data-linenumber="7121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7121
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<pre style="margin: 0;"> <span id="LC7121" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6871
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<td class="diff-line-num new_line" data-linenumber="7122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7122
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7122" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6872" 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">
6872
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<td class="diff-line-num new_line old" data-linenumber="7123" 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="LC6872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalMultiallelicHardcallFound</span><span class="p">))</span> <span class="p">{</span></span>
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7123
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<pre style="margin: 0;">+<span id="LC7123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalMultiallelicHardcallFound</span><span class="p">))</span> <span class="p">{</span></span>
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6873
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7124
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<pre style="margin: 0;"> <span id="LC7124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ctx.loaded_vrtypes</span></span>
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6874
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7125
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<pre style="margin: 0;"> <span id="LC7125" class="line" lang="cpp"> <span class="n" style="color: #333;">other_per_thread_cacheline_ct</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="p">(</span><span class="n" style="color: #333;">kPglVblockSize</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">);</span></span>
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6875
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7126
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<pre style="margin: 0;"> <span id="LC7126" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6885" style="width: 35px; color: rgba(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="7136" style="width: 35px; color: rgba(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">@@ -6885,19 +7136,19 @@ PglErr MakePlink2NoVsort(const char* xheader, const uintptr_t* sample_include, c</td>
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6885
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7136
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<pre style="margin: 0;"> <span id="LC7136" class="line" lang="cpp"> <span class="n" style="color: #333;">main_loadbufs</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;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">load_vblock_cacheline_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">));</span></span>
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6886
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<td class="diff-line-num new_line" data-linenumber="7137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7137
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<pre style="margin: 0;"> <span id="LC7137" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">loaded_vrtypes</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="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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6887
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<td class="diff-line-num new_line" data-linenumber="7138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7138
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<pre style="margin: 0;"> <span id="LC7138" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">loaded_vrtypes</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="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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6888
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<td class="diff-line-num new_line old" data-linenumber="7139" 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="LC6888" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalMultiallelicHardcallFound</span><span class="p">))</span> <span class="p">{</span></span>
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7139
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<pre style="margin: 0;">+<span id="LC7139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_dosage_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">read_gflags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalMultiallelicHardcallFound</span><span class="p">))</span> <span class="p">{</span></span>
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6889
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7140
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<pre style="margin: 0;"> <span id="LC7140" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">loaded_vrtypes</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">kPglVblockSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">calc_thread_ct</span><span class="p">));</span></span>
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6890
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<td class="diff-line-num new_line" data-linenumber="7141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7141
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<pre style="margin: 0;"> <span id="LC7141" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">loaded_vrtypes</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;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">kPglVblockSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">calc_thread_ct</span><span class="p">));</span></span>
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6891
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<td class="diff-line-num new_line" data-linenumber="7142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7142
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<pre style="margin: 0;"> <span id="LC7142" class="line" lang="cpp"> <span class="p">}</span></span>
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6892
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<td class="diff-line-num new_line old" data-linenumber="7143" 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="LC6892" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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7143
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<pre style="margin: 0;">+<span id="LC7143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_or_write_dosage_present</span><span class="p">)</span> <span class="p">{</span></span>
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6893
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<td class="diff-line-num new_line" data-linenumber="7144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7144
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<pre style="margin: 0;"> <span id="LC7144" class="line" lang="cpp"> <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;">bitvec_writebuf_byte_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToCachelineCt</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6894
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<td class="diff-line-num new_line" data-linenumber="7145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7145
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<pre style="margin: 0;"> <span id="LC7145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">dosagevals_writebuf_byte_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">kCacheline</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">;</span></span>
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6895
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7146
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<pre style="margin: 0;"> <span id="LC7146" class="line" lang="cpp"> <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;">tidx</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;">tidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">calc_thread_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">tidx</span><span class="p">)</span> <span class="p">{</span></span>
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6896
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<td class="diff-line-num new_line old" data-linenumber="7147" 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="LC6896" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7147" 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">
7147
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<pre style="margin: 0;">+<span id="LC7147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_or_write_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6897
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<td class="diff-line-num new_line" data-linenumber="7148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7148
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<pre style="margin: 0;"> <span id="LC7148" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phasepresents</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">bitvec_writebuf_byte_ct</span><span class="p">));</span></span>
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6898
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<td class="diff-line-num new_line" data-linenumber="7149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7149
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<pre style="margin: 0;"> <span id="LC7149" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_phaseinfos</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">bitvec_writebuf_byte_ct</span><span class="p">));</span></span>
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6899
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7150
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<pre style="margin: 0;"> <span id="LC7150" class="line" lang="cpp"></span>
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6900
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<td class="diff-line-num new_line old" data-linenumber="7151" 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="LC6900" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_<span class="idiff left right">h</span>phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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7151
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<pre style="margin: 0;">+<span id="LC7151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_phase_present</span><span class="p">)</span> <span class="p">{</span></span>
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6901
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7152
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<pre style="margin: 0;"> <span id="LC7152" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_all_hets</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw</span><span class="p">(</span><span class="n" style="color: #333;">BitCtToCachelineCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">));</span></span>
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6902
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7153
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<pre style="margin: 0;"> <span id="LC7153" class="line" lang="cpp"> <span class="p">}</span></span>
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6903
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7154
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<pre style="margin: 0;"> <span id="LC7154" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7438" style="width: 35px; color: rgba(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="7689" style="width: 35px; color: rgba(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">@@ -7438,7 +7689,7 @@ PglErr WritePvarResortedInterval(const ChrInfo* write_cip, const uint32_t* varia</td>
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7438
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7689
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<pre style="margin: 0;"> <span id="LC7689" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// allocation of buffers, and generating the header line occurs directly in</span></span>
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7439
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7690
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<pre style="margin: 0;"> <span id="LC7690" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// this function, while loading the next pvar_info_strs batch and writing the</span></span>
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7440
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7691
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<pre style="margin: 0;"> <span id="LC7691" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// next .pvar line batch are one level down.</span></span>
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7441
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<pre style="margin: 0;">-<span id="LC7441" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvarResorted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">write_cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_variant_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">thread_ct</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7442" 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="7692" 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">
7692
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<pre style="margin: 0;">+<span id="LC7692" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePvarResorted</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">write_cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">nonref_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_variant_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">)</span> <span class="p">{</span></span>
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7442
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<td class="diff-line-num new_line" data-linenumber="7693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7693
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7693" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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7443
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<td class="diff-line-num new_line" data-linenumber="7694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7694
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<pre style="margin: 0;"> <span id="LC7694" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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7444
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7695
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<pre style="margin: 0;"> <span id="LC7695" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7478" style="width: 35px; color: rgba(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="7729" style="width: 35px; color: rgba(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">@@ -7478,13 +7729,17 @@ PglErr WritePvarResorted(const char* outname, const char* xheader, const uintptr</td>
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7478
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<td class="diff-line-num new_line" data-linenumber="7729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7729
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<pre style="margin: 0;"> <span id="LC7729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarResorted_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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7479
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<td class="diff-line-num new_line" data-linenumber="7730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7730
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<pre style="margin: 0;"> <span id="LC7730" class="line" lang="cpp"> <span class="p">}</span></span>
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7480
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<td class="diff-line-num new_line" data-linenumber="7731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7731
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<pre style="margin: 0;"> <span id="LC7731" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="7481" 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="7732" 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">
7732
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<pre style="margin: 0;">+<span id="LC7732" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_filter</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 new_line" data-linenumber="7733" 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">
7733
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<pre style="margin: 0;">+<span id="LC7733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColFilter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7481" 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="7734" 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">
7734
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<pre style="margin: 0;">+<span id="LC7734" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7481" 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="7735" 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">
7735
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<pre style="margin: 0;">+<span id="LC7735" class="line" lang="cpp"> <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;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColMaybefilter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filter_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7481" 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="7736" 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">
7736
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<pre style="margin: 0;">+<span id="LC7736" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IntersectionIsEmpty</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7737" 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">
7737
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<pre style="margin: 0;">+<span id="LC7737" class="line" lang="cpp"> <span class="p">}</span></span>
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7481
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<td class="diff-line-num new_line" data-linenumber="7738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7738
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<pre style="margin: 0;"> <span id="LC7738" class="line" lang="cpp"> <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;">info_pr_flag_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">info_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfInfoPrFlagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7482" 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">
7482
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColXheader</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7483" 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">
7483
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">CsputsStd</span><span class="p">(</span><span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7484" 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">
7484
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarResorted_ret_WRITE_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7485" 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">
7485
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7485" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7486" 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">
7486
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7486" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7487" 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">
7487
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<td class="diff-line-num new_line old" data-linenumber="7739" 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="LC7487" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=PR,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Provisional reference allele, may not be based on real reference genome</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span> <span class="n" style="color: #333;">EOLN_STR</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="7488" 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="7739" 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">
7739
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<pre style="margin: 0;">+<span id="LC7739" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfPvarColXheader</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPvarColVcfheader</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7740" 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">
7740
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<pre style="margin: 0;">+<span id="LC7740" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PvarXheaderWrite</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">write_cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">,</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPvarColVcfheader</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;">write_filter</span><span class="p">,</span> <span class="n" style="color: #333;">write_info</span><span class="p">,</span> <span class="n" style="color: #333;">write_info_pr</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;">info_pr_flag_present</span><span class="p">),</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">kfUnsortedVar0</span><span class="p">,</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">css</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7741" 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">
7741
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<pre style="margin: 0;">+<span id="LC7741" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7742" 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">
7742
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<pre style="margin: 0;">+<span id="LC7742" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarResorted_ret_1</span><span class="p">;</span></span>
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7488
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7743
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<pre style="margin: 0;"> <span id="LC7743" class="line" lang="cpp"> <span class="p">}</span></span>
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7489
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7744
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<pre style="margin: 0;"> <span id="LC7744" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="7490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7490
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<td class="diff-line-num new_line" data-linenumber="7745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7745
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<pre style="margin: 0;"> <span id="LC7745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrset_source</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7502" style="width: 35px; color: rgba(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="7757" style="width: 35px; color: rgba(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">@@ -7502,12 +7757,6 @@ PglErr WritePvarResorted(const char* outname, const char* xheader, const uintptr</td>
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7502
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<td class="diff-line-num new_line" data-linenumber="7757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7757
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<pre style="margin: 0;"> <span id="LC7757" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="7503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7503
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7758
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<pre style="margin: 0;"> <span id="LC7758" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="7504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7504
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7759
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<pre style="margin: 0;"> <span id="LC7759" class="line" lang="cpp"></span>
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7505
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<td class="diff-line-num new_line old" data-linenumber="7760" 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="LC7505" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_filter</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 old old_line" data-linenumber="7506" 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">
7506
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<pre style="margin: 0;">-<span id="LC7506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColFilter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7507" 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">
7507
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<td class="diff-line-num new_line old" data-linenumber="7760" 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="LC7507" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7508" 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">
7508
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<td class="diff-line-num new_line old" data-linenumber="7760" 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="LC7508" class="line" lang="cpp"> <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;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPvarColMaybefilter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filter_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7509" 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">
7509
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<td class="diff-line-num new_line old" data-linenumber="7760" 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="LC7509" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IntersectionIsEmpty</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">filter_present</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7510" 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">
7510
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<pre style="margin: 0;">-<span id="LC7510" class="line" lang="cpp"> <span class="p">}</span></span>
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7511
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7760
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<pre style="margin: 0;"> <span id="LC7760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_filter</span><span class="p">)</span> <span class="p">{</span></span>
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7512
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<td class="diff-line-num new_line" data-linenumber="7761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7761
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<pre style="margin: 0;"> <span id="LC7761" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILTER"</span><span class="p">);</span></span>
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7513
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7762
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<pre style="margin: 0;"> <span id="LC7762" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7637" style="width: 35px; color: rgba(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="7886" style="width: 35px; color: rgba(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">@@ -7637,7 +7886,7 @@ PglErr WritePvarResorted(const char* outname, const char* xheader, const uintptr</td>
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7637
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7886
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<pre style="margin: 0;"> <span id="LC7886" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
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7887
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<pre style="margin: 0;"> <span id="LC7887" class="line" lang="cpp"><span class="p">}</span></span>
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7888
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<pre style="margin: 0;"> <span id="LC7888" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7640" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrIdx</span></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">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_nsort</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pvar_psam_flags</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7889" 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">
7889
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<pre style="margin: 0;">+<span id="LC7889" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrIdx</span></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">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_nsort</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="7641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7641
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<td class="diff-line-num new_line" data-linenumber="7890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7890
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<pre style="margin: 0;"> <span id="LC7890" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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7642
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7891
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<pre style="margin: 0;"> <span id="LC7891" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_end_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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7643
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7892
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<pre style="margin: 0;"> <span id="LC7892" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7843" style="width: 35px; color: rgba(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">@@ -7843,7 +8092,7 @@ PglErr MakePlink2Vsort(const char* xheader, const uintptr_t* sample_include, con</td>
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7843
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8092
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<pre style="margin: 0;"> <span id="LC8092" class="line" lang="cpp"> <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;">PgrGetNonrefFlags</span><span class="p">(</span><span class="n" style="color: #333;">simple_pgrp</span><span class="p">))</span> <span class="p">{</span></span>
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7844
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8093
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<pre style="margin: 0;"> <span id="LC8093" class="line" lang="cpp"> <span class="n" style="color: #333;">nonref_flags_storage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">PgrGetGflags</span><span class="p">(</span><span class="n" style="color: #333;">simple_pgrp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPgenGlobalAllNonref</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC8094" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC7846" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvarResorted</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_include</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="n" style="color: #333;"><span class="idiff">write_chr_info</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PgrGetNonrefFlags</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">simple_pgrp</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_thread_ct</span></span><span class="p">);</span></span>
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8095
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<pre style="margin: 0;">+<span id="LC8095" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePvarResorted</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">variant_include</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="n" style="color: #333;"><span class="idiff">write_chr_info</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PgrGetNonrefFlags</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">simple_pgrp</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nonref_flags_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">xheader</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC8096" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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7848
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8097
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<pre style="margin: 0;"> <span id="LC8097" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2Vsort_ret_1</span><span class="p">;</span></span>
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7849
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<pre style="margin: 0;"> <span id="LC8098" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#a125279a9188813c60a6fe3d56cead0bd36fcc8f"><strong>plink2_data.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,10 +64,18 @@ PglErr WriteMapOrBim(const char* outname, const uintptr_t* variant_include, cons</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarInfoOpenAndReloadHeader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">TextStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_reload_txsp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">line_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">info_col_idx_ptr</span><span class="p">);</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarInfoReload</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">,</span> <span class="n" style="color: #333;">TextStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_reload_txsp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">line_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">trs_variant_uidx_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarInfoReloadAndWrite</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_pr_flag_present</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">is_pr</span><span class="p">,</span> <span class="n" style="color: #333;">TextStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_reload_txsp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">line_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">write_iter_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rls_variant_uidx_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AppendChrsetLine</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">write_iter_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ChrLenLbound</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_variant_idx_to_old</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chr_fo_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">UnsortedVar</span> <span class="n" style="color: #333;">vpos_sortstatus</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// fileformat, fileDate, source</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes adequate buffer space</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AppendVcfHeaderStart</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v43</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cswritepp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteFam</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PedigreeIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">piip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">delim</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataFidColIsRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,9 +92,9 @@ void ApplyHardCallThresh(const uintptr_t* dosage_present, const Dosage* dosage_m</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ApplyHardCallThreshPhased</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dosage_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Dosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dosage_main</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">dosage_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hard_call_halfdist</span><span class="p">,</span> <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;">genovec</span><span class="p">,</span> <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;">phasepresent</span><span class="p">,</span> <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;">phaseinfo</span><span class="p">,</span> <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;">dphase_present</span><span class="p">,</span> <span class="n" style="color: #333;">SDosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dphase_delta</span><span class="p">,</span> <span class="n" style="color: #333;">SDosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_dphase_delta</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pgr_alloc_cacheline_ct</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" 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="LC95" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2NoVsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__maybe_unused</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">varid_multi_nonsnp_template_str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">missing_varid_match</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">UnsortedVar</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_variant_id_max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MiscFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">misc_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pgr_alloc_cacheline_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></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">xheader</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrIdx</span></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">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_nsort</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pvar_psam_flags</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MakePlink2Vsort</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uintptr_t</span></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">sample_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PedigreeIdInfo</span></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">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></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">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">variant_include</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrInfo</span></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">cip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></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">variant_bps</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">variant_ids</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_idx_offsets</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">allele_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">allele_presents</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">STD_ARRAY_PTR_DECL</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AlleleCode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refalt1_select</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_qual_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></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">pvar_quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_present</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></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">pvar_filter_npass</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">pvar_filter_storage</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">pvar_info_reload</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></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">variant_cms</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ChrIdx</span></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">chr_idxs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">xheader_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InfoFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_pheno_name_blen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">raw_variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variant_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_allele_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_filter_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_reload_slen</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_thread_ct</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hard_call_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dosage_erase_thresh</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MakePlink2Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_nsort</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PvarPsamFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pvar_psam_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">xheader</span></span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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91
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">SampleSortFileMap</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">new_sample_idx_to_old_ptr</span><span class="p">);</span></span>
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92
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>
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<li id="a1236d7e51efdf6705792595d24aa915967b7759">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#a1236d7e51efdf6705792595d24aa915967b7759"><strong>plink2_decompress.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,6 +88,7 @@ HEADER_INLINE unsigned char* TextStreamMemStart(TextStream* txs_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">GET_PRIVATE</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">txs_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">).</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">dst</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">}</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// TODO: logputs("\n") first when necessary</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TextErrPrint</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file_descrip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TextFileErrPrint</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file_descrip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">textFILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">txfp</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#0bb44e45468b97ef0c21ed5ca6767a690fbf6626"><strong>plink2_export.cc</strong></a>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#6414bd7aa55c6eef0319abf2a95e1f61296d37e8"><strong>plink2_export.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,7 +56,7 @@ void InitExportf(ExportfInfo* exportf_info_ptr);</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CleanupExportf</span><span class="p">(</span><span class="n" style="color: #333;">ExportfInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exportf_info_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Exportf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PedigreeIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">piip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">),</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_qual_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_quals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_filter_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_filter_npass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_filter_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExportfInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFlags</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_variant_id_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">MakePlink2Flags</span> <span class="n" style="color: #333;">make_plink2_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">pgr_alloc_cacheline_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Exportf</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PedigreeIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">piip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">),</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_qual_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_quals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_filter_present</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">pvar_filter_npass</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_filter_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ExportfInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">xheader_blen</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFlags</span> <span class="n" style="color: #333;">info_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_variant_id_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_filter_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_reload_slen</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">UnsortedVar</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vpos_sortstatus</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">MakePlink2Flags</span> <span class="n" style="color: #333;">make_plink2_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">pgr_alloc_cacheline_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader</span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace plink2</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4215,8 +4215,12 @@ PglErr SetRefalt1FromFile(const uintptr_t* variant_include, const char* const* v</td>
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4215
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4215
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<pre style="margin: 0;"> <span id="LC4215" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: "</span><span class="p">);</span></span>
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4216
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4216
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<pre style="margin: 0;"> <span id="LC4216" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// strlen("--ref-allele") == 12, strlen("--alt1-allele") == 13</span></span>
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4217
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4217
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<pre style="margin: 0;"> <span id="LC4217" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</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;">write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">flagstr</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">is_alt1</span><span class="p">);</span></span>
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4218
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<td class="diff-line-num new_line old" data-linenumber="4218" 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="LC4218" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">" mismatch for multiallelic variant '"</span><span class="p">);</span></span>
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4219
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<pre style="margin: 0;">-<span id="LC4219" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC4218" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">" mismatch for multiallelic variant"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4219" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If we put this all on one line, its length would be</span></span>
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<pre style="margin: 0;">+<span id="LC4220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 60 + is_alt1 + variant_id_slen. Split into two if this is >79.</span></span>
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4221
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<pre style="margin: 0;">+<span id="LC4221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">write_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">variant_id_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">is_alt1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">;</span></span>
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4222
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<pre style="margin: 0;">+<span id="LC4222" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">write_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\''</span><span class="p">;</span></span>
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4223
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<pre style="margin: 0;">+<span id="LC4223" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</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;">write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">variant_id_slen</span><span class="p">);</span></span>
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4220
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4224
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<pre style="margin: 0;"> <span id="LC4224" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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4221
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4225
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<pre style="margin: 0;"> <span id="LC4225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_mismatch_warning_ct</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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4222
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4226
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<pre style="margin: 0;"> <span id="LC4226" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputsb</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(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="132" style="width: 35px; color: rgba(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">@@ -132,8 +132,8 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="s" style="color: #d14;">" --bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="p">);</span></span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"vcf</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">bcf</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">keep-autoconv</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">help_ctrl</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"><span class="s" style="color: #d14;">" --keep-autoconv <span class="idiff left right"> : When importing non-PLINK-binary data, don't delete</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">autogenerated binary</span> fileset at end of run.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"><span class="s" style="color: #d14;">" --keep-autoconv <span class="idiff left right">['vzs'] : When importing non-PLINK-binary data, don't</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right"> delete autogenerated</span> fileset at end of run.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="p">);</span></span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"bfile</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">fam</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">no-fid</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">no-parents</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">no-sex</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">help_ctrl</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"><span class="s" style="color: #d14;">" --no-fid : .fam file does not contain column 1 (family ID).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="299" style="width: 35px; color: rgba(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="299" style="width: 35px; color: rgba(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">@@ -299,7 +299,7 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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299
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" --make-bed ['vzs'] [{trim-alts | erase-alt2+}]\n"</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['multiallelics='<split mode>]\n"</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"><span class="s" style="color: #d14;">" Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] +</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"><span class="s" style="color: #d14;">" Create a new PLINK <span class="idiff left right">2 </span>binary fileset (--make-pgen = .pgen + .pvar[.zst] +</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"><span class="s" style="color: #d14;">" .psam, --make-bpgen = .pgen + .bim[.zst] + .fam).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"><span class="s" style="color: #d14;">" * Unlike the automatic text-to-binary converters (which only heed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"><span class="s" style="color: #d14;">" chromosome filters), this supports all of PLINK's filtering flags.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -337,7 +337,7 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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337
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" * '+any': All variants with identical CHROM/POS/REF and no symbolic ALT\n"</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" alleles are joined into a single multiallelic variant.\n"</span></span>
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" Symbolic ALT alleles are joined separately. Additional conditions apply\n"</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" to them, and PLINK usually errors out when they aren't met.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" to them, and PLINK <span class="idiff left right">2 </span>usually errors out when they aren't met.\n"</span></span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" When splitting with 'vid-dup', the new variants keep the original variant\n"</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ID. Otherwise, new variant IDs are assigned as follows:\n"</span></span>
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 1. If --set-all-var-ids was specified, that template is applied.\n"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(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">@@ -372,6 +372,7 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"><span class="s" style="color: #d14;">" except for possibly FILTER/INFO definitions when those</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"><span class="s" style="color: #d14;">" column(s) have been removed. Without this, only the #CHROM</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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374
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"><span class="s" style="color: #d14;">" header line is kept.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"><span class="s" style="color: #d14;">" vcfheader: xheader, with additions to make it a valid VCF header.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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375
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"><span class="s" style="color: #d14;">" maybequal: QUAL. Omitted if all remaining values are missing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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376
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"><span class="s" style="color: #d14;">" qual: Force QUAL column to be written even when empty.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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377
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"><span class="s" style="color: #d14;">" maybefilter: FILTER. Omitted if all remaining values are missing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -414,8 +415,8 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['bits='<#>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"><span class="s" style="color: #d14;">" Create a new fileset with all filters applied. The following output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"><span class="s" style="color: #d14;">" formats are supported:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="cpp"><span class="s" style="color: #d14;">" (actually, only A, AD, A-transpose, b<span class="idiff left right">gen-1.x, ind-major-bed, haps</span>,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">hapslegen</span>d, oxford, and vcf are implemented for now)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"><span class="s" style="color: #d14;">" (actually, only A, AD, A-transpose, b<span class="idiff left right">cf, bgen-1.x, haps, hapslegend</span>,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">ind-major-be</span>d, oxford, and vcf are implemented for now)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"><span class="s" style="color: #d14;">" * '23': 23andMe 4-column format. This can only be used on a single</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"><span class="s" style="color: #d14;">" sample's data (--keep may be handy), and does not support</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"><span class="s" style="color: #d14;">" multicharacter allele codes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -466,15 +467,18 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"><span class="s" style="color: #d14;">" --tfile.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'vcf', : VCF (default version 4.3). If PAR1 and PAR2 are present,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"><span class="s" style="color: #d14;">" 'vcf-4.2'<span class="idiff left right"> </span> they are automatically merged with chrX, with proper</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right"> </span> handling of chromosome codes and male ploidy.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right"> </span> When the 'bgz' modifier is present, the VCF file is</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="cpp"><span class="s" style="color: #d14;">" block-gzipped.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"><span class="s" style="color: #d14;">" 'vcf-4.2'<span class="idiff left right">,</span> they are automatically merged with chrX, with proper</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">'bcf',</span> handling of chromosome codes and male ploidy.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">'bcf-4.2'</span> When the 'bgz' modifier is present, the VCF file is</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"><span class="s" style="color: #d14;">" block-gzipped.<span class="idiff left right"> (This always happens with BCF output.)</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"><span class="s" style="color: #d14;">" The 'id-paste' modifier controls which .psam columns are</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"><span class="s" style="color: #d14;">" used to construct sample IDs (choices are maybefid, fid,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"><span class="s" style="color: #d14;">" iid, maybesid, and sid; default is maybefid,iid,maybesid),</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"><span class="s" style="color: #d14;">" while the 'id-delim' modifier sets the character between the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp"><span class="s" style="color: #d14;">" ID pieces (default '_').</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"><span class="s" style="color: #d14;">" Genotypes are always exported. If you want to export a</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"><span class="s" style="color: #d14;">" sites-only VCF instead, see --make-pgen/--make-just-pvar's</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"><span class="s" style="color: #d14;">" 'vcfheader' column set.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"><span class="s" style="color: #d14;">" Dosages are not exported unless the 'vcf-dosage=' modifier</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"><span class="s" style="color: #d14;">" is present. The following five dosage export modes are</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"><span class="s" style="color: #d14;">" supported:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<li id="21274e2b169d6e71a254a974b86ae7af8acdf275">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#21274e2b169d6e71a254a974b86ae7af8acdf275"><strong>plink2_import.cc</strong></a>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#d029425224aa0cc89613ddc5656608ce6488e765"><strong>plink2_import.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,8 +28,9 @@ namespace plink2 {</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImport0</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportKeepAutoconv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportDoubleId</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportVcfRequireGt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportKeepAutoconvVzs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportDoubleId</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">kfImportVcfRequireGt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</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="LC34" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">ImportFlags</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#f5d85292088358ebd24c2a15cd3a9b7759ba61c9"><strong>plink2_matrix.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -447,10 +447,19 @@ HEADER_INLINE void PrintSymmFmatrix(const float* matrix, uint32_t dim) {</td>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PrintMatrix</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">dim</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <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;">uii</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;">uii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dim</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <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;">ujj</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;">ujj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dim</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ujj</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%g "</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</span><span class="p">[</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ujj</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PrintMatrix</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">row_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">col_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ulii</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;">ulii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">row_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ulii</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">uljj</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;">uljj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">col_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uljj</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%g "</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</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;">col_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uljj</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PrintFmatrix</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">row_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">col_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">stride</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ulii</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;">ulii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">row_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ulii</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">uljj</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;">uljj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">col_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uljj</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%g "</span><span class="p">,</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="n" style="color: #333;">matrix</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;">stride</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uljj</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/77ea05fd7558352b0652f5254e5f8a9949668165...a4645c27ae1a3d3dcdaa84e6c35f62512f438e8c#9e0620cca890479e38d176e292c73012d6b0f630"><strong>plink2_matrix_calc.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -442,7 +442,12 @@ PglErr KingCutoffBatch(const SampleIdInfo* siip, uint32_t raw_sample_ct, double</td>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">fsize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">fsize_double_expected</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Invalid --king-cutoff .bin file size (expected %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" or %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" bytes).</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;">fsize_double_expected</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;">fsize_double_expected</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">fsize_double_square</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">king_id_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">S_CAST</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;">king_id_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">fsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fsize_double_square</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">fsize</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fsize_double_square</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --king-cutoff currently requires a *triangular* .bin file; the provided</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">file appears to be square.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Invalid --king-cutoff .bin file size (expected %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" or %"</span> <span class="n" style="color: #333;">PRIu64</span> <span class="s" style="color: #d14;">" bytes).</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;">fsize_double_expected</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;">fsize_double_expected</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">KingCutoffBatch_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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447
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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448
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">king_id_ct</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">((</span><span class="mh" style="color: #099;">0x7ffff000</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -787,7 +787,8 @@ PglErr LoadPvar(const char* pvarname, const char* var_filter_exceptions_flattene</td>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// probable todo: load INFO:END. (does this allow the CNV module to be</span></span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// unified with the rest of the program?) but this will probably wait</span></span>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// until I need to analyze some sort of CNV data, and that day keeps</span></span>
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790
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// getting postponed...</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// getting postponed... for now, the BCF exporter performs its own parsing</span></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of INFO:END so that it can fill each variant's rlen field correctly.</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// possible todo: require FILTER to only contain values declared in header,</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and modify its storage accordingly? (pointless for now, but worthwhile</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// to keep an eye on what typical VCF files look like.)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -833,7 +834,7 @@ PglErr LoadPvar(const char* pvarname, const char* var_filter_exceptions_flattene</td>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_alloc_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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834
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">g_bigstack_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bigstack_mark</span><span class="p">;</span></span>
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835
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;"><span class="idiff left right">kfPvarColXheader</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">xheader_needed</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_mark</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xheader_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">kfPvarColXheader</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">kfPvarColVcfheader</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">xheader_needed</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_mark</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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837
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrset_present</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="LC839" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_pr_present</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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839
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_pr_nonflag_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="907" style="width: 35px; color: rgba(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">@@ -906,7 +907,6 @@ PglErr LoadPvar(const char* pvarname, const char* var_filter_exceptions_flattene</td>
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906
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp"> <span class="n" style="color: #333;">line_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span><span class="p">;</span></span>
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907
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="cpp"> <span class="p">}</span></span>
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908
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="cpp"> <span class="p">}</span></span>
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909
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_flags_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">InfoFlags</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">info_pr_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoPrFlagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">info_pr_nonflag_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoPrNonflagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">info_nonpr_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoNonprPresent</span><span class="p">));</span></span>
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910
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp"> <span class="n" style="color: #333;">line_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">line_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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911
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="cpp"> <span class="p">}</span></span>
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912
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xheader_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="927" style="width: 35px; color: rgba(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="927" style="width: 35px; color: rgba(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">@@ -927,6 +927,7 @@ PglErr LoadPvar(const char* pvarname, const char* var_filter_exceptions_flattene</td>
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927
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_present</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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928
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cm_col_present</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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929
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line_start</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 class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="930" 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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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_flags_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="n" style="color: #333;">InfoFlags</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">info_pr_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoPrFlagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">info_pr_nonflag_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoPrNonflagPresent</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">info_nonpr_present</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfInfoNonprPresent</span><span class="p">));</span></span>
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930
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parse header</span></span>
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931
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [-1] = #CHROM (must be first column)</span></span>
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932
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [0] = POS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1388" style="width: 35px; color: rgba(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="1389" style="width: 35px; color: rgba(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">@@ -1388,10 +1389,14 @@ PglErr LoadPvar(const char* pvarname, const char* var_filter_exceptions_flattene</td>
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1388
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1389
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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="cpp"> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_file_order</span><span class="p">[</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">chrs_encountered_m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_chr_code</span><span class="p">;</span></span>
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1389
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp"> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chrs_encountered_m1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">;</span></span>
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1390
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr_idx_to_foidx</span><span class="p">[</span><span class="n" style="color: #333;">cur_chr_code</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrs_encountered_m1</span><span class="p">;</span></span>
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1391
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<pre style="margin: 0;">-<span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">last_bp</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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1392
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1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">last_cm</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">DBL_MAX</span><span class="p">;</span></span>
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1393
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1393
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<pre style="margin: 0;"> <span id="LC1393" class="line" lang="cpp"> <span class="p">}</span></span>
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1394
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1394
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="cpp"> <span class="p">}</span></span>
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1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// always need to set this, if we want to avoid chromosome-length</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// overestimation in --sort-vars + early-variant-filter +</span></span>
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1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pvar-cols=+vcfheader case.</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp"> <span class="n" style="color: #333;">last_bp</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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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="cpp"></span>
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1395
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1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">cur_chr_code</span><span class="p">,</span> <span class="n" style="color: #333;">loaded_chr_mask</span><span class="p">);</span></span>
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1396
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1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chr_output_name_buf</span><span class="p">)</span> <span class="p">{</span></span>
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1397
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1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">chr_name_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrtoa</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">cur_chr_code</span><span class="p">,</span> <span class="n" style="color: #333;">chr_output_name_buf</span><span class="p">);</span></span>
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