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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/dd37e023c02f02fe4e642e2009742df7f5c7295f">dd37e023</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2021-07-23T21:49:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-210701+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/52ff17d8b3b8e3cfd419d9a236d9b2c55f3ccdfc">52ff17d8</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2021-07-23T21:49:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.00_a3-210701+dfsg'
Update to upstream version '2.00~a3-210701+dfsg'
with Debian dir 1a532024f15d7baeaed7a5c3387acd594edc4880</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/d2773ed43c23f74d0db64432442fb669681849cf">d2773ed4</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2021-07-23T21:50:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump d/changelog
</pre>
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<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#386f23c017c84fb5b75ce96dbac305abca500153">
include/pgenlib_misc.cc
</a>
</li>
<li class="file-stats">
<a href="#e77f6102ff6675b5bc8947f913bdad39d3e254f4">
include/pgenlib_misc.h
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<li class="file-stats">
<a href="#4776c94d0e4a55582487ac9c960d27e25dcb2101">
include/pgenlib_read.cc
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<li class="file-stats">
<a href="#1188c77f6805f7e4384fc1c8aff83aa49781bacc">
include/pgenlib_read.h
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<li class="file-stats">
<a href="#4b320ace526dc39d7e8f303b1481e411020379dc">
include/plink2_string.cc
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<li class="file-stats">
<a href="#e04ad6b4524c358c1efeb53be9496b769cc2fe19">
include/plink2_string.h
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<li class="file-stats">
<a href="#c0e8350b8eabd8ac9d4590b796469c56bb9b025f">
include/plink2_text.cc
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<li class="file-stats">
<a href="#4a91cf0fe31504c3f2e1c3b908af3d0c89bc167f">
include/plink2_text.h
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<li class="file-stats">
<a href="#4561030caec1f631dc9e4107a4ef154548d13cb0">
pgen_compress.cc
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<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
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<li class="file-stats">
<a href="#5c0ac48ba397674ac28142efc3b29b7de442d076">
plink2_cmdline.cc
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<li class="file-stats">
<a href="#353424a9b88ab7aad403c3734bdd60f28af6b661">
plink2_cmdline.h
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<li class="file-stats">
<a href="#576e4fd14d1d66b779bb9f5d05d29f2871392d1a">
plink2_common.h
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<li class="file-stats">
<a href="#49a9b8ad832d31a64af7997ab4dff296fe4603bc">
plink2_data.cc
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<li class="file-stats">
<a href="#a125279a9188813c60a6fe3d56cead0bd36fcc8f">
plink2_data.h
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<li class="file-stats">
<a href="#0bb44e45468b97ef0c21ed5ca6767a690fbf6626">
plink2_export.cc
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<li class="file-stats">
<a href="#55e5eafcebf3678e6c9ea25cbbd0a648bf3c272b">
plink2_fasta.cc
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<li class="file-stats">
<a href="#82c8c0946825d16815c68e845955a90079d70b6b">
plink2_glm.cc
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<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
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<li class="file-stats">
<a href="#21274e2b169d6e71a254a974b86ae7af8acdf275">
plink2_import.cc
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<li class="file-stats">
<a href="#77152f1b1412f42b6493e48b39abf3be847a626f">
plink2_merge.cc
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<li class="file-stats">
<a href="#59216b3409d1d2c9ff4b9a784709ac15d3a3e12c">
plink2_merge.h
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<li class="file-stats">
<a href="#68ec2c295201ac9d061fcfc37744eba392732614">
plink2_misc.cc
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</li>
<li class="file-stats">
<a href="#436d5ebb95c2149ac987678ddff33cffca2ea965">
plink2_psam.cc
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<li class="file-stats">
<a href="#112cb73bff359b837852d2266ec756df9e6637d8">
plink2_pvar.cc
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<li class="file-stats">
<a href="#60a6a1f914f822f6625c37a46f38a9ace19230bc">
plink2_pvar.h
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink2 (2.00~a3-210701+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Fri, 23 Jul 2021 21:49:33 +0200</span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">plink2 (2.00~a3-210203+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<li id="386f23c017c84fb5b75ce96dbac305abca500153">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#386f23c017c84fb5b75ce96dbac305abca500153"><strong>include/pgenlib_misc.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(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="122" style="width: 35px; color: rgba(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">@@ -122,7 +122,7 @@ void CopyGenomatchSubset(const uintptr_t* __restrict raw_bitarr, const uintptr_t</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Variant of ExpandBytearr() which is based off a target 2-bit value instead</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// of single expand_mask bits. expand_size must be the number of instance of</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// of single expand_mask bits. expand_size must be the number of instance<span class="idiff left right">s</span> of</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// the target value in genovec.</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ExpandBytearrFromGenoarr</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;">compact_bitarr</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;">uint32_t</span> <span class="n" style="color: #333;">genoword_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">expand_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">read_start_bit</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;">target</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC128" 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;">expand_sizex_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expand_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read_start_bit</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">@@ -726,6 +726,23 @@ void GenoarrCountFreqsUnsafe(const uintptr_t* genoarr, uint32_t sample_ct, STD_A</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"> <span class="n" style="color: #333;">genocounts</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;">bothset_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MostCommonGenoUnsafe</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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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">STD_ARRAY_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">genocounts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">GenoarrCountFreqsUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">genoarr</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">genocounts</span><span class="p">);</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">most_common_geno_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="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC734" 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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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="p">}</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">most_common_geno</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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737
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<pre style="margin: 0;">+<span id="LC737" 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;">cur_geno</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;">cur_geno</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;">cur_geno</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="n" style="color: #333;">cur_geno</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">most_common_geno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_geno</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="n" style="color: #333;">cur_geno</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">most_common_geno</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// geno_vvec now allowed to be unaligned.</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CountSubset3FreqVec6</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">geno_vvec</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">interleaved_mask_vvec</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vec_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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">even_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">odd_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">bothset_ctp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">vec_ct</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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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -232,6 +232,10 @@ void Count3FreqVec6(const VecW* geno_vvec, uint32_t vec_ct, uint32_t* __restrict</td>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// vector-alignment preferred.</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenoarrCountFreqsUnsafe</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="n" style="color: #333;">STD_ARRAY_REF</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">genocounts</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// GenoarrCountsFreqsUnsafe() wrapper that returns most common genotype,</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// breaking ties in favor of the lower value.</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">MostCommonGenoUnsafe</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>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// geno_vvec now allowed to be unaligned.</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CountSubset3FreqVec6</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">geno_vvec</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">interleaved_mask_vvec</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vec_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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">even_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">odd_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">bothset_ctp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -2696,8 +2696,7 @@ void CopyAndSubsetDifflist(const uintptr_t* __restrict sample_include, const uin</td>
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<pre style="margin: 0;"> <span id="LC2696" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Populates pgrp->ldbase_genovec or</span></span>
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<pre style="margin: 0;"> <span id="LC2697" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// pgrp->ldbase_{raregeno,difflist_sample_ids,difflist_len}, depending on</span></span>
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<pre style="margin: 0;"> <span id="LC2698" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// storage type.</span></span>
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<pre style="margin: 0;">-<span id="LC2699" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Currently just called by ReadDifflistOrGenovecSubsetUnsafe(), which isn't</span></span>
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<pre style="margin: 0;">-<span id="LC2700" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// exploited by plink2 yet.</span></span>
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<pre style="margin: 0;">+<span id="LC2699" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Currently just called by ReadDifflistOrGenovecSubsetUnsafe().</span></span>
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<pre style="margin: 0;"> <span id="LC2700" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">LdLoadMinimalSubsetIfNecessary</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="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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">sample_include_cumulative_popcounts</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;">vidx</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReaderMain</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgrp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2701" 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;">LdLoadNecessary</span><span class="p">(</span><span class="n" style="color: #333;">vidx</span><span class="p">,</span> <span class="n" style="color: #333;">pgrp</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2702" 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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<li id="1188c77f6805f7e4384fc1c8aff83aa49781bacc">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#1188c77f6805f7e4384fc1c8aff83aa49781bacc"><strong>include/pgenlib_read.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">@@ -277,6 +277,14 @@ HEADER_INLINE unsigned char* PgrGetVrtypes(PgenReader* pgr_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pgrp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">vrtypes</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC280" 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;">PgrGetVrtype</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgr_ptr</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="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PgenReaderMain</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgrp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</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;">pgr_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pgrp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">vrtypes</span><span class="p">)</span> <span class="p">{</span></span>
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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="n" style="color: #333;">pgrp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">vrtypes</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="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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pgrp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">const_vrtype</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC288" 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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">PgrGetNonrefFlags</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;">pgr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">PgenReaderMain</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgrp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</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;">pgr_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pgrp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">nonref_flags</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -219,52 +219,41 @@ void WordWrap(uint32_t suffix_len, char* strbuf) {</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC222" 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;">uint32_t</span> <span class="n" style="color: #333;">kPow10</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="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">100000</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span> <span class="mi" style="color: #099;">100000000</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000000</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// This implementation is from Kendall Willets. See</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// https://lemire.me/blog/2021/06/03/computing-the-number-of-digits-of-an-integer-even-faster/</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_AVX2</span></span>
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<pre style="margin: 0;">-<span id="LC225" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kLzUintSlenBase</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"><span class="p">{</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</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="LC232" class="line" lang="cpp"> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"> <span class="mi" style="color: #099;">1</span><span class="p">};</span> <span class="c1" style="color: #998; font-style: italic;">// UintSlen(0) needs to be 1, not zero</span></span>
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<pre style="margin: 0;">+<span id="LC226" 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;">uint64_t</span> <span class="n" style="color: #333;">kLzcntUintSlenTable</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="p">{</span><span class="mi" style="color: #099;">42949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">42949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span> <span class="mi" style="color: #099;">4294967296LL</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">UintSlen</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC236" 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;">lz_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_lzcnt_u32</span><span class="p">(</span><span class="n" style="color: #333;">num</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC238" 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_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kLzUintSlenBase</span><span class="p">[</span><span class="n" style="color: #333;">lz_ct</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">slen_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kPow10</span><span class="p">[</span><span class="n" style="color: #333;">slen_base</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kLzcntUintSlenTable</span><span class="p">[</span><span class="n" style="color: #333;">lz_ct</span><span class="p">])</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC239" 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="LC242" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// could also use something like ((32 - lz_ct) * 77) >> 8, since 77/256 is a</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// sufficiently good approximation of ln(2)/ln(10), but that's a bit slower and</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// this table doesn't take much space</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bugfix (29 Mar 2018): this table was totally wrong, ugh</span></span>
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<pre style="margin: 0;">-<span id="LC247" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">kBsrUintSlenBase</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"><span class="p">{</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC240" 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;">uint64_t</span> <span class="n" style="color: #333;">kBsrUintSlenTable</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="p">{</span><span class="mi" style="color: #099;">4294967296LL</span><span class="p">,</span> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span> <span class="mi" style="color: #099;">8589934582LL</span><span class="p">,</span> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span> <span class="mi" style="color: #099;">12884901788LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span> <span class="mi" style="color: #099;">17179868184LL</span><span class="p">,</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">21474826480LL</span><span class="p">,</span> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span> <span class="mi" style="color: #099;">25769703776LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span> <span class="mi" style="color: #099;">30063771072LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">34349738368LL</span><span class="p">,</span> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span> <span class="mi" style="color: #099;">38554705664LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">41949672960LL</span><span class="p">,</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="mi" style="color: #099;">42949672960LL</span><span class="p">,</span> <span class="mi" style="color: #099;">42949672960LL</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">UintSlen</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tried divide-by-10 and divide-by-100 loops, they were slower</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// also tried a hardcoded binary tree, it was better but still slower</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bsru32(0) is undefined</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num</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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<pre style="margin: 0;">-<span id="LC263" 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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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">num</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="LC255" 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;">top_bit_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bsru32</span><span class="p">(</span><span class="n" style="color: #333;">num</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC266" 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_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kBsrUintSlenBase</span><span class="p">[</span><span class="n" style="color: #333;">top_bit_pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">slen_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kPow10</span><span class="p">[</span><span class="n" style="color: #333;">slen_base</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kBsrUintSlenTable</span><span class="p">[</span><span class="n" style="color: #333;">top_bit_pos</span><span class="p">])</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC258" 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="LC259" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -596,6 +596,11 @@ HEADER_INLINE void StrptrArrNsort(uintptr_t ct, const char** strptr_arr) {</td>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">StrNsortDeref</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">strptr_arr</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">StrNsortDeref</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">strptr_arr</span><span class="p">)[</span><span class="n" style="color: #333;">ct</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Considered adding stable-sort variants of StrptrArrSort, but looks like it's</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// usually better to define a more sophisticated comparator that removes the</span></span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// need for the explicit stable-sort. (Note that std::stable_sort can throw</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// std::bad_alloc, etc.)</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// need to expose these for plink2_cmdline bigstack-allocating</span></span>
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SortStrboxIndexed()'s use</span></span>
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SortStrbox32bFinish</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">str_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_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">use_nsort</span><span class="p">,</span> <span class="n" style="color: #333;">Strbuf28Ui</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filled_wkspace</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;">sorted_strbox</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;">id_map</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#c0e8350b8eabd8ac9d4590b796469c56bb9b025f"><strong>include/plink2_text.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">@@ -98,6 +98,7 @@ BoolErr GzRawInit(const void* buf, uint32_t nbytes, GzRawDecompressStream* gzp)</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" 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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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="p">}</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ds_initialized</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="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</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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102
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<pre style="margin: 0;"> <span id="LC102" 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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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><span class="p">}</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"></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">@@ -316,45 +317,68 @@ BoolErr IsPathologicallyLongLineOrToken(const char* line_start, const char* load</td>
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316
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<pre style="margin: 0;"> <span id="LC317" 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;">kShortErrRfileTruncatedGz</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GzRawStreamRead: gzipped file appears to be truncated"</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"></span>
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318
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">GzRawStreamRead</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_end</span><span class="p">,</span> <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;">ff</span><span class="p">,</span> <span class="n" style="color: #333;">GzRawDecompressStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gzp</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_iterp</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;">errmsgp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">z_stream</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dsp</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="n" style="color: #333;"><span class="idiff">gzp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ds</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">(</span>(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">feof_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gzp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">eof</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// </span>(!dsp->avail_in) && feof_unlocked(ff)) {</span></span>
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321
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<pre style="margin: 0;"> <span id="LC322" 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="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="n" style="color: #333;">z_stream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dsp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ds</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC325" 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_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_iterp</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">;</span></span>
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326
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// can be zero after TextRewind()</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_out</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;">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;">dst_iter</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="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dst_iter</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="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="p">,</span> <span class="n" style="color: #333;">Z_SYNC_FLUSH</span><span class="p">);</span></span>
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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;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_NEED_DICT</span><span class="p">)))</span> <span class="p">{</span></span>
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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="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">msg</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">msg</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC333" 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="LC334" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zError</span><span class="p">(</span><span class="n" style="color: #333;">zerr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</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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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_out</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;">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;">dst_iter</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="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dst_iter</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="p">,</span> <span class="n" style="color: #333;">Z_SYNC_FLUSH</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="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;">zerr</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_NEED_DICT</span><span class="p">)))</span> <span class="p">{</span></span>
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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;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">msg</span><span class="p">)</span> <span class="p">{</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">msg</span><span class="p">;</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" 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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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zError</span><span class="p">(</span><span class="n" style="color: #333;">zerr</span><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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetDecompressFail</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;">dst_iter</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;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_out</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_STREAM_END</span><span class="p">)</span> <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;">break</span><span class="p">;</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <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="c1" style="color: #998; font-style: italic;">// bugfix (25 May 2021): may need to open a new stream, or skip</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// trailing garbage</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">trailing_byte_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">trailing_byte_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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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;">trailing_byte_ct</span><span class="p">)</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="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in</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;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_in</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC351" 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;">nbytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread_unlocked</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in</span><span class="p">[</span><span class="n" style="color: #333;">trailing_byte_ct</span><span class="p">]),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">kDecompressChunkSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trailing_byte_ct</span><span class="p">,</span> <span class="n" style="color: #333;">ff</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trailing_byte_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nbytes</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetDecompressFail</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;">if</span> <span class="p">((</span><span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</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;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_in</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="mi" style="color: #099;">31</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_in</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="mi" style="color: #099;">139</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// EOF or trailing garbage</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</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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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_iterp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_iter</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC359" 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="LC360" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NDEBUG</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="n" style="color: #333;">dsp</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="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">errcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">errcode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC366" 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="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">dst_iter</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;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_out</span><span class="p">);</span></span>
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339
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">dst_iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">dst_end</span><span class="p">);</span></span>
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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="p">}</span></span>
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343
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"> <span class="p">}</span></span>
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372
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<pre style="margin: 0;"> <span id="LC372" 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;">nbytes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">kDecompressChunkSize</span><span class="p">,</span> <span class="n" style="color: #333;">ff</span><span class="p">);</span></span>
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345
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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346
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">dsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbytes</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="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;">nbytes</span><span class="p">)</span> <span class="p">{</span></span>
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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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">unlikely</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nbytes</span><span class="p">)<span class="idiff right">)</span></span> <span class="p">{</span></span>
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348
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376
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<pre style="margin: 0;"> <span id="LC376" 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;">feof_unlocked</span><span class="p">(</span><span class="n" style="color: #333;">ff</span><span class="p">)))</span> <span class="p">{</span></span>
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349
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">);</span></span>
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350
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetReadFail</span><span class="p">;</span></span>
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351
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379
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<pre style="margin: 0;"> <span id="LC379" 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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">zerr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">))</span> <span class="p">{</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kShortErrRfileTruncatedGz</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;">return</span> <span class="n" style="color: #333;">kPglRetDecompressFail</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="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="c1" style="color: #998; font-style: italic;">// Normal EOF.</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errmsgp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kShortErrRfileTruncatedGz</span><span class="p">;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetDecompressFail</span><span class="p">;</span></span>
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358
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">dst_iter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dst_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst_iterp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_iter</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">@@ -391,12 +415,12 @@ PglErr ZstRawStreamRead(char* dst_end, FILE* ff, ZstRawDecompressStream* zstp, c</td>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetReadFail</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">zstp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ib</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">zstp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ib</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbytes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_inbytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </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">nbytes</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">unlikely</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">n_inbytes</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">errmsgp</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">kShortErrZstdPrefixUnknown</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kPglRetDecompressFail</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"> <span class="idiff left"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_</span>size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbytes</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_inbytes</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">zstp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</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">new_size</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// bugfix (28 Feb 2021): Possible for nbytes to be zero at the same time</span></span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// n_inbytes is positive when e.g. the input .zst file is the concatenation</span></span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// of multiple ordinary .zst files, which is permitted by the spec.</span></span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </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">new_size</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;"> <span id="LC424" 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="LC425" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <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">@@ -678,6 +702,7 @@ void TextFileRewind(textFILE* txf_ptr) {</td>
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678
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">basep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">file_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kFileUncompressed</span><span class="p">)</span> <span class="p">{</span></span>
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679
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">basep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">file_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kFileGzip</span><span class="p">)</span> <span class="p">{</span></span>
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680
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">txfp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rds</span><span class="p">.</span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</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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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="n" style="color: #333;">txfp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rds</span><span class="p">.</span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">eof</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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681
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NDEBUG</span></span>
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682
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txfp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rds</span><span class="p">.</span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">ds</span><span class="p">);</span></span>
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683
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1171" style="width: 35px; color: rgba(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="1196" style="width: 35px; color: rgba(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">@@ -1171,6 +1196,7 @@ THREAD_FUNC_DECL TextStreamThread(void* raw_arg) {</td>
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1171
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kFileUncompressed</span><span class="p">)</span> <span class="p">{</span></span>
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1172
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kFileGzip</span><span class="p">)</span> <span class="p">{</span></span>
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1173
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="cpp"> <span class="n" style="color: #333;">rdsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</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="new_line diff-line-num new" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="cpp"> <span class="n" style="color: #333;">rdsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">eof</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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1174
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NDEBUG</span></span>
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1175
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"> <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rdsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gz</span><span class="p">.</span><span class="n" style="color: #333;">ds</span><span class="p">);</span></span>
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1176
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1283" style="width: 35px; color: rgba(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">@@ -1257,6 +1283,7 @@ THREAD_FUNC_DECL TextStreamThread(void* raw_arg) {</td>
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1257
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kFileGzip</span><span class="p">:</span></span>
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1258
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="p">{</span></span>
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1259
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">GzRawDecompressStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gzp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rdsp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gz</span><span class="p">;</span></span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</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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1260
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1287
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">z_stream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dsp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gzp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ds</span><span class="p">;</span></span>
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1261
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1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NDEBUG</span></span>
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1262
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="cpp"> <span class="n" style="color: #333;">inflateReset</span><span class="p">(</span><span class="n" style="color: #333;">dsp</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#4a91cf0fe31504c3f2e1c3b908af3d0c89bc167f"><strong>include/plink2_text.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">@@ -150,6 +150,7 @@ typedef struct GzRawDecompressStreamStruct {</td>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" 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;">in</span><span class="p">;</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">ds</span><span class="p">;</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ds_initialized</span><span class="p">;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">eof</span><span class="p">;</span></span>
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153
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">GzRawDecompressStream</span><span class="p">;</span></span>
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154
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BgzfRawDecompressStream declared in plink2_bgzf.h.</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#4561030caec1f631dc9e4107a4ef154548d13cb0"><strong>pgen_compress.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">@@ -30,9 +30,9 @@ int32_t main(int32_t argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">argc</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;">argc</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>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="s" style="color: #d14;">"Usage:</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="LC33" class="line" lang="cpp"><span class="s" style="color: #d14;">"pgen_compress <span class="idiff left">[</span>input .bed or .pgen<span class="idiff">] [</span>output filename<span class="idiff">] {</span>sample_ct<span class="idiff right">}</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="LC33" class="line" lang="cpp"><span class="s" style="color: #d14;">"pgen_compress <span class="idiff left"><</span>input .bed or .pgen<span class="idiff">> <</span>output filename<span class="idiff">> [</span>sample_ct<span class="idiff right">]</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="s" style="color: #d14;">" (sample_ct is required when loading a .bed file)</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="LC35" class="line" lang="cpp"><span class="s" style="color: #d14;">"pgen_compress -u <span class="idiff left">[</span>input .pgen<span class="idiff">] [</span>output .bed<span class="idiff right">]</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="LC35" class="line" lang="cpp"><span class="s" style="color: #d14;">"pgen_compress -u <span class="idiff left"><</span>input .pgen<span class="idiff">> <</span>output .bed<span class="idiff right">></span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" 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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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -71,7 +71,7 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="">#ifdef USE_MKL</span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang=""> " Intel"</span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="">#endif</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang=""> " (<span class="idiff left right">3 Feb</span> 2021)";</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang=""> " (<span class="idiff left right">1 Jul</span> 2021)";</span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="">static const char ver_str2[] =</span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang=""> " "</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">@@ -999,9 +999,17 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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999
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999
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<pre style="margin: 0;"> <span id="LC999" class="line" lang=""> goto Plink2Core_ret_NOMEM;</span>
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1000
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang=""> }</span>
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1001
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang=""> const uint32_t nonref_flags_already_loaded = (nonref_flags != nullptr);</span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang=""> if ((!nonref_flags) && ((header_ctrl & 192) == 192)) {</span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang=""> if (unlikely(bigstack_alloc_w(raw_variant_ctl, &nonref_flags))) {</span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang=""> goto Plink2Core_ret_NOMEM;</span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang=""> if (!nonref_flags_already_loaded) {</span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang=""> const uint32_t nonref_flags_status_shifted = header_ctrl & 192;</span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang=""> if (nonref_flags_status_shifted == 192) {</span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang=""> if (unlikely(bigstack_alloc_w(raw_variant_ctl, &nonref_flags))) {</span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang=""> goto Plink2Core_ret_NOMEM;</span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang=""> }</span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang=""> } else if ((pgfi.const_vrtype != kPglVrtypePlink1) && (!nonref_flags_status_shifted)) {</span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang=""> // This should never happen with a chain of plink2-generated .pgen</span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang=""> // files, but it's permitted by the specification and makes future</span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang=""> // merge unsafe.</span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang=""> logerrputs("Warning: .pgen file indicates that provisional-REF information is stored in the\ncompanion .pvar, but that .pvar lacks either an INFO/PR header or an INFO\ncolumn. Assuming all REF alleles are correct.\n");</span>
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1005
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang=""> }</span>
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1006
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang=""> }</span>
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1007
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang=""> pgfi.nonref_flags = nonref_flags;</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2892" style="width: 35px; color: rgba(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">@@ -2884,8 +2892,6 @@ uint32_t CmdlineSingleChr(const ChrInfo* cip, MiscFlags misc_flags) {</td>
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2884
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2892
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<pre style="margin: 0;"> <span id="LC2892" class="line" lang="">}</span>
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2885
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2893
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<pre style="margin: 0;"> <span id="LC2893" class="line" lang=""></span>
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2886
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2894
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<pre style="margin: 0;"> <span id="LC2894" class="line" lang="">void GetExportfTargets(const char* const* argvk, uint32_t param_ct, ExportfFlags* exportf_flags_ptr, IdpasteFlags* exportf_id_paste_ptr, uint64_t* format_param_idxs_ptr) {</span>
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2887
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<pre style="margin: 0;">-<span id="LC2887" class="line" lang=""> // does not error out if no format present, since this is needed for --recode</span>
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2888
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<pre style="margin: 0;">-<span id="LC2888" class="line" lang=""> // translation</span>
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2889
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2895
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<pre style="margin: 0;"> <span id="LC2895" class="line" lang=""> // supports multiple formats</span>
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2890
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2896
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<pre style="margin: 0;"> <span id="LC2896" class="line" lang=""> uint64_t format_param_idxs = 0;</span>
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2891
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2897
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<pre style="margin: 0;"> <span id="LC2897" class="line" lang=""> for (uint32_t param_idx = 1; param_idx <= param_ct; ++param_idx) {</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2984,7 +2990,9 @@ void GetExportfTargets(const char* const* argvk, uint32_t param_ct, ExportfFlags</td>
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2984
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2990
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<pre style="margin: 0;"> <span id="LC2990" class="line" lang=""> }</span>
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2985
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2991
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<pre style="margin: 0;"> <span id="LC2991" class="line" lang=""> case 'o':</span>
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2986
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2992
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<pre style="margin: 0;"> <span id="LC2992" class="line" lang=""> if (!strcmp(cur_modif2, "xford")) {</span>
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2987
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<pre style="margin: 0;">-<span id="LC2987" class="line" lang=""> cur_format = kfExportfOxGen;</span>
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2993
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<pre style="margin: 0;">+<span id="LC2993" class="line" lang=""> cur_format = kfExportfOxGenV1;</span>
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2994
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<pre style="margin: 0;">+<span id="LC2994" class="line" lang=""> } else if (!strcmp(cur_modif2, "xford-v2")) {</span>
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2995
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<pre style="margin: 0;">+<span id="LC2995" class="line" lang=""> cur_format = kfExportfOxGenV2;</span>
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2988
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2996
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<pre style="margin: 0;"> <span id="LC2996" class="line" lang=""> }</span>
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2989
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2997
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<pre style="margin: 0;"> <span id="LC2997" class="line" lang=""> break;</span>
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2990
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2998
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<pre style="margin: 0;"> <span id="LC2998" class="line" lang=""> case 'p':</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3022" style="width: 35px; color: rgba(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">@@ -3014,7 +3022,7 @@ void GetExportfTargets(const char* const* argvk, uint32_t param_ct, ExportfFlags</td>
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3014
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3022
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<pre style="margin: 0;"> <span id="LC3022" class="line" lang=""> } else if (!strcmp(&(cur_modif2[2]), "-4.2")) {</span>
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3015
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<td class="new_line diff-line-num" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3023
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<pre style="margin: 0;"> <span id="LC3023" class="line" lang=""> cur_format = kfExportfVcf42;</span>
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3016
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<td class="new_line diff-line-num" data-linenumber="3024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3024
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<pre style="margin: 0;"> <span id="LC3024" class="line" lang=""> } else if ((!strcmp(&(cur_modif2[2]), "-fid")) || (!strcmp(&(cur_modif2[2]), "-iid"))) {</span>
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3017
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<td class="new_line diff-line-num old" data-linenumber="3025" style="width: 35px; color: rgba(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="LC3017" class="line" lang=""> <span class="idiff left">sn</span>printf(<span class="idiff right">g_logbuf, kLogbufSize, </span>"Note: --export 'v%s' modifier is deprecated. Use 'vcf' + 'id-paste=%s'.\n", cur_modif2, &(cur_modif2[3]));</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3025
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<pre style="margin: 0;">+<span id="LC3025" class="line" lang=""> <span class="idiff left right">log</span>printf("Note: --export 'v%s' modifier is deprecated. Use 'vcf' + 'id-paste=%s'.\n", cur_modif2, &(cur_modif2[3]));</span>
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3018
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<td class="new_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3026
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<pre style="margin: 0;"> <span id="LC3026" class="line" lang=""> cur_format = kfExportfVcf43;</span>
</pre>
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3019
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<td class="new_line diff-line-num" data-linenumber="3027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3027
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<pre style="margin: 0;"> <span id="LC3027" class="line" lang=""> *exportf_id_paste_ptr = (cur_modif2[3] == 'f')? kfIdpasteFid : kfIdpasteIid;</span>
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3020
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3028
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<pre style="margin: 0;"> <span id="LC3028" class="line" lang=""> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3443" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3443,21 +3451,9 @@ int main(int argc, char** argv) {</td>
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3443
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3451
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<pre style="margin: 0;"> <span id="LC3451" class="line" lang=""> break;</span>
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3444
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3452
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<pre style="margin: 0;"> <span id="LC3452" class="line" lang=""> case 'r':</span>
</pre>
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3445
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3453
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<pre style="margin: 0;"> <span id="LC3453" class="line" lang=""> if (strequal_k(flagname_p, "recode", flag_slen)) {</span>
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3446
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<pre style="margin: 0;">-<span id="LC3446" class="line" lang=""> // special case: translate to "export ped" if no format specified</span>
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<td class="old_line diff-line-num old" data-linenumber="3447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3447
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<td class="new_line diff-line-num old" data-linenumber="3454" style="width: 35px; color: rgba(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="LC3447" class="line" lang=""> const uint32_t param_ct = GetParamCt(argvk, argc, arg_idx);</span>
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<td class="old_line diff-line-num old" data-linenumber="3448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3448
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<td class="new_line diff-line-num old" data-linenumber="3454" style="width: 35px; color: rgba(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="LC3448" class="line" lang=""> if (unlikely(param_ct > 4)) {</span>
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3449
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<td class="new_line diff-line-num old" data-linenumber="3454" style="width: 35px; color: rgba(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="LC3449" class="line" lang=""> fputs("Error: --recode accepts at most 4 arguments.\n", stderr);</span>
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3450
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<pre style="margin: 0;">-<span id="LC3450" class="line" lang=""> goto main_ret_INVALID_CMDLINE;</span>
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3451
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<pre style="margin: 0;">-<span id="LC3451" class="line" lang=""> }</span>
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3452
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<pre style="margin: 0;">-<span id="LC3452" class="line" lang=""> ExportfFlags dummy;</span>
</pre>
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3453
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<pre style="margin: 0;">-<span id="LC3453" class="line" lang=""> IdpasteFlags dummy2;</span>
</pre>
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3454
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<pre style="margin: 0;">-<span id="LC3454" class="line" lang=""> uint64_t format_param_idxs;</span>
</pre>
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3455
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<pre style="margin: 0;">-<span id="LC3455" class="line" lang=""> GetExportfTargets(&(argvk[arg_idx]), param_ct, &dummy, &dummy2, &format_param_idxs);</span>
</pre>
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3456
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<pre style="margin: 0;">-<span id="LC3456" class="line" lang=""> if (!format_param_idxs) {</span>
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3457
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<pre style="margin: 0;">-<span id="LC3457" class="line" lang=""> snprintf(flagname_write_iter, kMaxFlagBlen, "export ped");</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3458
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<pre style="margin: 0;">-<span id="LC3458" class="line" lang=""> } else {</span>
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3459
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<td class="new_line diff-line-num old" data-linenumber="3454" style="width: 35px; color: rgba(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=""> snprintf(flagname_write_iter, kMaxFlagBlen, "export");</span>
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3460
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<td class="new_line diff-line-num old" data-linenumber="3454" style="width: 35px; color: rgba(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="LC3460" class="line" lang=""> }</span>
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3454
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<pre style="margin: 0;">+<span id="LC3454" class="line" lang=""> // don't bother translating no-modifier --recode to "--export ped",</span>
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3455
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<pre style="margin: 0;">+<span id="LC3455" class="line" lang=""> // just let it fail</span>
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3456
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<pre style="margin: 0;">+<span id="LC3456" class="line" lang=""> snprintf(flagname_write_iter, kMaxFlagBlen, "export");</span>
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3461
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<td class="new_line diff-line-num" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3457
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<pre style="margin: 0;"> <span id="LC3457" class="line" lang=""> } else if (strequal_k(flagname_p, "remove-founders", flag_slen)) {</span>
</pre>
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3462
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<td class="new_line diff-line-num" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3458
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<pre style="margin: 0;"> <span id="LC3458" class="line" lang=""> snprintf(flagname_write_iter, kMaxFlagBlen, "keep-founders");</span>
</pre>
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3463
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3459
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<pre style="margin: 0;"> <span id="LC3459" class="line" lang=""> } else if (strequal_k(flagname_p, "remove-nonfounders", flag_slen)) {</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4658" style="width: 35px; color: rgba(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="4654" style="width: 35px; color: rgba(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">@@ -4658,21 +4654,16 @@ int main(int argc, char** argv) {</td>
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4658
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4654
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<pre style="margin: 0;"> <span id="LC4654" class="line" lang=""> goto main_ret_1;</span>
</pre>
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4659
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4655
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<pre style="margin: 0;"> <span id="LC4655" class="line" lang=""> }</span>
</pre>
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4660
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4656
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<pre style="margin: 0;"> <span id="LC4656" class="line" lang=""> pc.filter_flags |= kfFilterPvarReq;</span>
</pre>
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4661
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<pre style="margin: 0;">-<span id="LC4661" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "xport")<span class="idiff left right"> || strequal_k_unsafe(flagname_p2, "xport ped")</span>) {</span>
</pre>
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4657
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<pre style="margin: 0;">+<span id="LC4657" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "xport")) {</span>
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4662
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4658
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<pre style="margin: 0;"> <span id="LC4658" class="line" lang=""> // todo: determine actual limit</span>
</pre>
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4663
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4659
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<pre style="margin: 0;"> <span id="LC4659" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 0, 50))) {</span>
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4664
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4660
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<pre style="margin: 0;"> <span id="LC4660" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
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4665
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4661
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<pre style="margin: 0;"> <span id="LC4661" class="line" lang=""> }</span>
</pre>
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4666
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4662
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<pre style="margin: 0;"> <span id="LC4662" class="line" lang=""> uint64_t format_param_idxs = 0;</span>
</pre>
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4667
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<pre style="margin: 0;">-<span id="LC4667" class="line" lang=""> if (!flagname_p2[5]) {</span>
</pre>
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4668
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<td class="new_line diff-line-num old" data-linenumber="4663" style="width: 35px; color: rgba(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="LC4668" class="line" lang=""> GetExportfTargets(&(argvk[arg_idx]), param_ct, &pc.exportf_info.flags, &pc.exportf_info.idpaste_flags, &format_param_idxs);</span>
</pre>
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4669
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<td class="new_line diff-line-num old" data-linenumber="4663" style="width: 35px; color: rgba(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="LC4669" class="line" lang=""> if (unlikely(!format_param_idxs)) {</span>
</pre>
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4670
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<pre style="margin: 0;">-<span id="LC4670" class="line" lang=""> logerrputs("Error: --export requires at least one output format. (Did you forget 'ped' or\n'vcf'?)\n");</span>
</pre>
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4671
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<pre style="margin: 0;">-<span id="LC4671" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
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4672
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<pre style="margin: 0;">-<span id="LC4672" class="line" lang=""> }</span>
</pre>
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4673
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<td class="new_line diff-line-num old" data-linenumber="4663" style="width: 35px; color: rgba(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="LC4673" class="line" lang=""> logputsb();</span>
</pre>
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4674
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<td class="new_line diff-line-num old" data-linenumber="4663" style="width: 35px; color: rgba(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="LC4674" class="line" lang=""> } else {</span>
</pre>
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4675
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<td class="new_line diff-line-num old" data-linenumber="4663" style="width: 35px; color: rgba(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="LC4675" class="line" lang=""> pc.exportf_info.flags = kfExportfPed;</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4663
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<pre style="margin: 0;">+<span id="LC4663" class="line" lang=""> GetExportfTargets(&(argvk[arg_idx]), param_ct, &pc.exportf_info.flags, &pc.exportf_info.idpaste_flags, &format_param_idxs);</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4664
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<pre style="margin: 0;">+<span id="LC4664" class="line" lang=""> if (unlikely(!format_param_idxs)) {</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4665
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<pre style="margin: 0;">+<span id="LC4665" class="line" lang=""> logerrputs("Error: --export requires at least one output format. (Did you forget 'ped' or\n'vcf'?)\n");</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="4666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4666
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<pre style="margin: 0;">+<span id="LC4666" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4676
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<td class="new_line diff-line-num" data-linenumber="4667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4667
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<pre style="margin: 0;"> <span id="LC4667" class="line" lang=""> }</span>
</pre>
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4677
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<td class="new_line diff-line-num" data-linenumber="4668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4668
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<pre style="margin: 0;"> <span id="LC4668" class="line" lang=""> // can't have e.g. bgen-1.1 and bgen-1.2 simultaneously, since they</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4678
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<td class="new_line diff-line-num" data-linenumber="4669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4669
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4669" class="line" lang=""> // have the same extension and different content.</span>
</pre>
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</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4689" style="width: 35px; color: rgba(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="4680" style="width: 35px; color: rgba(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">@@ -4689,6 +4680,10 @@ int main(int argc, char** argv) {</td>
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4689
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<td class="new_line diff-line-num" data-linenumber="4680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4680
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4680" class="line" lang=""> logerrputs("Error: 'A' and 'AD' formats cannot be exported simultaneously.\n");</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4690
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<td class="new_line diff-line-num" data-linenumber="4681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4681
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4681" class="line" lang=""> goto main_ret_INVALID_CMDLINE;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4691
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<td class="new_line diff-line-num" data-linenumber="4682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4682
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4682" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="4692" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="4683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4683
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<pre style="margin: 0;">+<span id="LC4683" class="line" lang=""> if (unlikely((pc.exportf_info.flags & (kfExportfOxGenV1 | kfExportfOxGenV2)) == (kfExportfOxGenV1 | kfExportfOxGenV2))) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="4692" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="4684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4684
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4684" class="line" lang=""> logerrputs("Error: 'oxford' and 'oxford-v2' formats cannot be exported simultaneously.\n");</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="4692" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="4685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4685
</td>
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<pre style="margin: 0;">+<span id="LC4685" class="line" lang=""> goto main_ret_INVALID_CMDLINE;</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="4692" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="4686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4686
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<pre style="margin: 0;">+<span id="LC4686" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4692
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<td class="new_line diff-line-num" data-linenumber="4687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4687
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4687" class="line" lang=""> for (uint32_t param_idx = 1; param_idx <= param_ct; ++param_idx) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4693
</td>
<td class="new_line diff-line-num" data-linenumber="4688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4688
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4688" class="line" lang=""> // could use AdvBoundedTo0Bit()...</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4694
</td>
<td class="new_line diff-line-num" data-linenumber="4689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4689
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4689" class="line" lang=""> if ((format_param_idxs >> param_idx) & 1) {</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5799" style="width: 35px; color: rgba(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="5794" style="width: 35px; color: rgba(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">@@ -5799,7 +5794,7 @@ int main(int argc, char** argv) {</td>
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<td class="old_line diff-line-num" data-linenumber="5799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5799
</td>
<td class="new_line diff-line-num" data-linenumber="5794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5794
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5794" class="line" lang=""> logerrputs("Error: Multiple --het cols= modifiers.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="5800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5800
</td>
<td class="new_line diff-line-num" data-linenumber="5795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5795
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5795" class="line" lang=""> goto main_ret_INVALID_CMDLINE;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="5801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5801
</td>
<td class="new_line diff-line-num" data-linenumber="5796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5796
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5796" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="5802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5802
</td>
<td class="new_line diff-line-num old" data-linenumber="5797" style="width: 35px; color: rgba(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="LC5802" class="line" lang=""> reterr = ParseColDescriptor(&(cur_modif[5]), "maybefid\0fid\0maybesid\0sid\0hom\0het\0nobs\0f\0", "het", kfH<span class="idiff left">ardyColChrom</span>, kfH<span class="idiff">ardy</span>ColDefault, 1, &pc.h<span class="idiff right">ardy</span>_flags);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="5803" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="5797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5797
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5797" class="line" lang=""> reterr = ParseColDescriptor(&(cur_modif[5]), "maybefid\0fid\0maybesid\0sid\0hom\0het\0nobs\0f\0", "het", kfH<span class="idiff left">etColMaybefid</span>, kfH<span class="idiff">et</span>ColDefault, 1, &pc.h<span class="idiff right">et</span>_flags);</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="5803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5803
</td>
<td class="new_line diff-line-num" data-linenumber="5798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5798
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5798" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="5804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5804
</td>
<td class="new_line diff-line-num" data-linenumber="5799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5799
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5799" class="line" lang=""> goto main_ret_1;</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="5805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5805
</td>
<td class="new_line diff-line-num" data-linenumber="5800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5800
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5800" class="line" lang=""> }</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7801" style="width: 35px; color: rgba(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="7796" style="width: 35px; color: rgba(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">@@ -7801,7 +7796,7 @@ int main(int argc, char** argv) {</td>
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<td class="old_line diff-line-num" data-linenumber="7801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7801
</td>
<td class="new_line diff-line-num" data-linenumber="7796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7796
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7796" class="line" lang=""> const char* cur_modif = argvk[arg_idx + 1];</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7802
</td>
<td class="new_line diff-line-num" data-linenumber="7797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7797
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7797" class="line" lang=""> const uint32_t cur_modif_slen = strlen(cur_modif);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7803
</td>
<td class="new_line diff-line-num" data-linenumber="7798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7798
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7798" class="line" lang=""> if (strequal_k(cur_modif, "erase", cur_modif_slen)) {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7804
</td>
<td class="new_line diff-line-num old" data-linenumber="7799" style="width: 35px; color: rgba(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="LC7804" class="line" lang=""> if (unlikely(pmerge_info.merge_info_mode != kMerge<span class="idiff left right">Qic</span>ModeErase)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7805" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7799
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7799" class="line" lang=""> if (unlikely(pmerge_info.merge_info_mode != kMerge<span class="idiff left right">InfoCm</span>ModeErase)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7805
</td>
<td class="new_line diff-line-num" data-linenumber="7800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7800
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7800" class="line" lang=""> logerrputs("Error: \"--merge-xheader-mode erase\" requires \"--merge-info-mode erase\".\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7806
</td>
<td class="new_line diff-line-num" data-linenumber="7801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7801
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7801" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7807
</td>
<td class="new_line diff-line-num" data-linenumber="7802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7802
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7802" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7815" style="width: 35px; color: rgba(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="7810" style="width: 35px; color: rgba(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">@@ -7815,34 +7810,24 @@ int main(int argc, char** argv) {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7815
</td>
<td class="new_line diff-line-num" data-linenumber="7810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7810
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7810" class="line" lang=""> } else if (unlikely(strequal_k_unsafe(flagname_p2, "erge-equal-pos"))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7816
</td>
<td class="new_line diff-line-num" data-linenumber="7811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7811
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7811" class="line" lang=""> logerrputs("Error: --merge-equal-pos has been retired. Use e.g. --set-all-var-ids before\nmerging instead.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7817
</td>
<td class="new_line diff-line-num" data-linenumber="7812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7812
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7812" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7818
</td>
<td class="new_line diff-line-num old" data-linenumber="7813" style="width: 35px; color: rgba(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="LC7818" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-qual-mode") ||</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7819
</td>
<td class="new_line diff-line-num old" data-linenumber="7813" style="width: 35px; color: rgba(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="LC7819" class="line" lang=""> strequal_k_unsafe(flagname_p2, "erge-info-mode") ||</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7820
</td>
<td class="new_line diff-line-num old" data-linenumber="7813" style="width: 35px; color: rgba(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="LC7820" class="line" lang=""> strequal_k_unsafe(flagname_p2, "erge-cm-mode")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7821" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7813
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7813" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-qual-mode")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7821
</td>
<td class="new_line diff-line-num" data-linenumber="7814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7814
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7814" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7822
</td>
<td class="new_line diff-line-num" data-linenumber="7815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7815
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7815" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7823
</td>
<td class="new_line diff-line-num" data-linenumber="7816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7816
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7816" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7824
</td>
<td class="new_line diff-line-num" data-linenumber="7817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7817
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7817" class="line" lang=""> const char* cur_modif = argvk[arg_idx + 1];</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7825
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<td class="new_line diff-line-num" data-linenumber="7818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7818
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<pre style="margin: 0;"> <span id="LC7818" class="line" lang=""> const uint32_t cur_modif_slen = strlen(cur_modif);</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7826
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<td class="new_line diff-line-num old" data-linenumber="7819" style="width: 35px; color: rgba(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="LC7826" class="line" lang=""> MergeQicMode mode;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7827
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<td class="new_line diff-line-num" data-linenumber="7819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7819
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7819" class="line" lang=""> if (strequal_k(cur_modif, "erase", cur_modif_slen)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7828
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<td class="new_line diff-line-num old" data-linenumber="7820" style="width: 35px; color: rgba(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="LC7828" class="line" lang=""> mode = kMergeQ<span class="idiff left right">ic</span>ModeErase;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7829" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7820
</td>
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<pre style="margin: 0;">+<span id="LC7820" class="line" lang=""> <span class="idiff left">pmerge_info.merge_qual_</span>mode = kMergeQ<span class="idiff right">ual</span>ModeErase;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7829
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<td class="new_line diff-line-num" data-linenumber="7821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7821
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7821" class="line" lang=""> } else if (strequal_k(cur_modif, "nm-match", cur_modif_slen)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7830
</td>
<td class="new_line diff-line-num old" data-linenumber="7822" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7830" class="line" lang=""> mode = kMergeQ<span class="idiff left right">ic</span>ModeNmMatch;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7831" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7822
</td>
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<pre style="margin: 0;">+<span id="LC7822" class="line" lang=""> <span class="idiff left">pmerge_info.merge_qual_</span>mode = kMergeQ<span class="idiff right">ual</span>ModeNmMatch;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7831
</td>
<td class="new_line diff-line-num" data-linenumber="7823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7823
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7823" class="line" lang=""> } else if (strequal_k(cur_modif, "nm-first", cur_modif_slen)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7832
</td>
<td class="new_line diff-line-num old" data-linenumber="7824" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7832" class="line" lang=""> mode = kMergeQ<span class="idiff left right">ic</span>ModeNmFirst;</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7833
</td>
<td class="new_line diff-line-num old" data-linenumber="7824" style="width: 35px; color: rgba(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="LC7833" class="line" lang=""> } else if <span class="idiff left">(likely</span>(strequal_k(cur_modif, "first", cur_modif_slen))<span class="idiff right">)</span> {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7834
</td>
<td class="new_line diff-line-num old" data-linenumber="7824" style="width: 35px; color: rgba(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="LC7834" class="line" lang=""> mode = kMergeQ<span class="idiff left right">ic</span>ModeFirst;</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7835
</td>
<td class="new_line diff-line-num old" data-linenumber="7824" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7835" class="line" lang=""> } else {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7836
</td>
<td class="new_line diff-line-num old" data-linenumber="7824" style="width: 35px; color: rgba(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="LC7836" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --<span class="idiff left">%s</span> argument '%s'.\n", <span class="idiff right">flagname_p, </span>cur_modif);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7837" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7824
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7824" class="line" lang=""> <span class="idiff left">pmerge_info.merge_qual_</span>mode = kMergeQ<span class="idiff right">ual</span>ModeNmFirst;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7837" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7825
</td>
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<pre style="margin: 0;">+<span id="LC7825" class="line" lang=""> } else if (strequal_k(cur_modif, "first", cur_modif_slen)) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7837" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7826
</td>
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<pre style="margin: 0;">+<span id="LC7826" class="line" lang=""> <span class="idiff left">pmerge_info.merge_qual_</span>mode = kMergeQ<span class="idiff right">ual</span>ModeFirst;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7837" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7827
</td>
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<pre style="margin: 0;">+<span id="LC7827" class="line" lang=""> } else <span class="idiff left right">if (unlikely(!strequal_k(cur_modif, "min", cur_modif_slen))) </span>{</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7837" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7828
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7828" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --<span class="idiff left right">merge-qual-mode</span> argument '%s'.\n", cur_modif);</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7837
</td>
<td class="new_line diff-line-num" data-linenumber="7829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7829
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7829" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7838
</td>
<td class="new_line diff-line-num" data-linenumber="7830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7830
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7830" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7839
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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="LC7839" class="line" lang=""> if (flagname_p2[5] == 'q') {</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7840
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7840" class="line" lang=""> pmerge_info.merge_qual_mode = mode;</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7841
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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="LC7841" class="line" lang=""> } else if (flagname_p2[5] == 'i') {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7842
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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="LC7842" class="line" lang=""> pmerge_info.merge_info_mode = mode;</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7843
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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="LC7843" class="line" lang=""> } else {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7844
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<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7844" class="line" lang=""> pmerge_info.merge_cm_mode = mode;</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7845
</td>
<td class="new_line diff-line-num old" data-linenumber="7831" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7845" class="line" lang=""> }</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7846
</td>
<td class="new_line diff-line-num" data-linenumber="7831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7831
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7831" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-filter-mode")) {</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7847
</td>
<td class="new_line diff-line-num" data-linenumber="7832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7832
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7832" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7848
</td>
<td class="new_line diff-line-num" data-linenumber="7833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7833
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7833" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7861" style="width: 35px; color: rgba(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="7846" style="width: 35px; color: rgba(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">@@ -7861,6 +7846,31 @@ int main(int argc, char** argv) {</td>
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<td class="old_line diff-line-num" data-linenumber="7861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7861
</td>
<td class="new_line diff-line-num" data-linenumber="7846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7846
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7846" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --merge-filter-mode argument '%s'.\n", cur_modif);</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7862
</td>
<td class="new_line diff-line-num" data-linenumber="7847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7847
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7847" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7863
</td>
<td class="new_line diff-line-num" data-linenumber="7848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7848
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7848" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7849
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7849" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-info-mode") ||</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7850
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7850" class="line" lang=""> strequal_k_unsafe(flagname_p2, "erge-cm-mode")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7851
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7851" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7852
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7852" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7853
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7853" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7854
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7854" class="line" lang=""> const char* cur_modif = argvk[arg_idx + 1];</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7855
</td>
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<pre style="margin: 0;">+<span id="LC7855" class="line" lang=""> const uint32_t cur_modif_slen = strlen(cur_modif);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7856
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7856" class="line" lang=""> MergeInfoCmMode mode;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7857
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7857" class="line" lang=""> if (strequal_k(cur_modif, "erase", cur_modif_slen)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7858
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7858" class="line" lang=""> mode = kMergeInfoCmModeErase;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7859
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7859" class="line" lang=""> } else if (strequal_k(cur_modif, "nm-match", cur_modif_slen)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7860
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7860" class="line" lang=""> mode = kMergeInfoCmModeNmMatch;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7861
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7861" class="line" lang=""> } else if (strequal_k(cur_modif, "nm-first", cur_modif_slen)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7862
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7862" class="line" lang=""> mode = kMergeInfoCmModeNmFirst;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7863
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7863" class="line" lang=""> } else if (likely(strequal_k(cur_modif, "first", cur_modif_slen))) {</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7864
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7864" class="line" lang=""> mode = kMergeInfoCmModeFirst;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7865
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7865" class="line" lang=""> } else {</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7866
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7866" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --%s argument '%s'.\n", flagname_p, cur_modif);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7867
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7867" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7868
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7868" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7869
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7869" class="line" lang=""> if (flagname_p2[5] == 'i') {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7870
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7870" class="line" lang=""> pmerge_info.merge_info_mode = mode;</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7871
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7871" class="line" lang=""> } else {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7872
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7872" class="line" lang=""> pmerge_info.merge_cm_mode = mode;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7864" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7873
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7873" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7864
</td>
<td class="new_line diff-line-num" data-linenumber="7874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7874
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7874" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-info-sort") ||</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7865
</td>
<td class="new_line diff-line-num" data-linenumber="7875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7875
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7875" class="line" lang=""> strequal_k_unsafe(flagname_p2, "erge-pheno-sort")) {</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7866
</td>
<td class="new_line diff-line-num" data-linenumber="7876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7876
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7876" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8546" style="width: 35px; color: rgba(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="8556" style="width: 35px; color: rgba(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">@@ -8546,6 +8556,48 @@ int main(int argc, char** argv) {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8546
</td>
<td class="new_line diff-line-num" data-linenumber="8556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8556
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8556" class="line" lang=""> goto main_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8547
</td>
<td class="new_line diff-line-num" data-linenumber="8557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8557
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8557" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8548
</td>
<td class="new_line diff-line-num" data-linenumber="8558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8558
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8558" class="line" lang=""> pc.command_flags1 |= kfCommand1Pmerge;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8559
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8559" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "merge-list-dir")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8560
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8560" class="line" lang=""> if (unlikely((!(pc.command_flags1 & kfCommand1Pmerge)) || (!pmerge_info.list_fname))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8561
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8561" class="line" lang=""> logerrputs("Error: --pmerge-list-dir must be used with --pmerge-list.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8562
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8562" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8563
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8563" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8564
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8564" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8565
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8565" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8566
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8566" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8567
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8567" class="line" lang=""> const char* dir_str = argvk[arg_idx + 1];</span>
</pre>
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</tr>
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</td>
<td class="new_line diff-line-num new" data-linenumber="8568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8568
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8568" class="line" lang=""> const uint32_t dir_slen = strlen(dir_str);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8569
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8569" class="line" lang=""> uint32_t append_path_sep = 0;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8570
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8570" class="line" lang="">#ifdef _WIN32</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8571
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8571" class="line" lang=""> const char path_sep = '\\';</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8572
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8572" class="line" lang=""> if ((dir_str[dir_slen - 1] != '/') && (dir_str[dir_slen - 1] != '\\')) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8573
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8573" class="line" lang=""> append_path_sep = 1;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8574
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8574" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8575
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8575" class="line" lang="">#else</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8576
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8576" class="line" lang=""> const char path_sep = '/';</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8577
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8577" class="line" lang=""> if (dir_str[dir_slen - 1] != '/') {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8578
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8578" class="line" lang=""> append_path_sep = 1;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8579
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8579" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8580
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8580" class="line" lang="">#endif</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8581
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8581" class="line" lang=""> const uint32_t alloc_blen = dir_slen + 1 + append_path_sep;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8582
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8582" class="line" lang=""> if (unlikely(alloc_blen > (kPglFnamesize - 9))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8583
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8583" class="line" lang=""> logerrputs("Error: --pmerge-list-dir argument too long.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8584
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8584" class="line" lang=""> goto main_ret_OPEN_FAIL;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8585
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8585" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8586
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8586" class="line" lang=""> if (unlikely(pgl_malloc(alloc_blen, &pmerge_info.list_base_dir))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8587
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8587" class="line" lang=""> goto main_ret_NOMEM;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8588
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8588" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8589
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8589" class="line" lang=""> char* write_iter = memcpya(pmerge_info.list_base_dir, dir_str, dir_slen);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8590
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8590" class="line" lang=""> if (append_path_sep) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8591
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8591" class="line" lang=""> *write_iter++ = path_sep;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8592
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8592" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8593
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8593" class="line" lang=""> *write_iter = '\0';</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8594
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8594" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "merge-output-vzs")) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8595
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8595" class="line" lang=""> if (unlikely(!(pc.command_flags1 & kfCommand1Pmerge))) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8596
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8596" class="line" lang=""> logerrputs("Error: --pmerge-output-vzs must be used with --pmerge or --pmerge-list.\n");</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8597
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8597" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8598
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8598" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8599
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8599" class="line" lang=""> pmerge_info.flags |= kfPmergeOutputVzs;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="8549" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="8600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8600
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8600" class="line" lang=""> goto main_param_zero;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8549
</td>
<td class="new_line diff-line-num" data-linenumber="8601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8601
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8601" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "gen-diff")) {</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8550
</td>
<td class="new_line diff-line-num" data-linenumber="8602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8602
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8602" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 7))) {</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="8551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8551
</td>
<td class="new_line diff-line-num" data-linenumber="8603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8603
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8603" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10565" style="width: 35px; color: rgba(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="10617" style="width: 35px; color: rgba(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">@@ -10565,7 +10617,7 @@ int main(int argc, char** argv) {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10565
</td>
<td class="new_line diff-line-num" data-linenumber="10617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10617
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10617" class="line" lang=""> const uint32_t no_samples_ok = !((pc.dependency_flags & (kfFilterAllReq | kfFilterPsamReq)) || (pc.command_flags1 & kfCommand1Pmerge));</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10566
</td>
<td class="new_line diff-line-num" data-linenumber="10618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10618
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10618" class="line" lang=""> const uint32_t is_vcf = (xload / kfXloadVcf) & 1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10567
</td>
<td class="new_line diff-line-num" data-linenumber="10619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10619
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10619" class="line" lang=""> pvar_is_compressed = ((import_flags & (kfImportKeepAutoconv | kfImportKeepAutoconvVzs)) != kfImportKeepAutoconv);</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10568
</td>
<td class="new_line diff-line-num old" data-linenumber="10620" style="width: 35px; color: rgba(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="LC10568" class="line" lang=""> if (no_samples_ok && is_vcf && (!(import_flags & kfImportKeepAutoconv)) && pc.command_flags1) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10569" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="10620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10620
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10620" class="line" lang=""> if (no_samples_ok && is_vcf && (!(import_flags & <span class="idiff left">(</span>kfImportKeepAutoconv<span class="idiff right"> | kfImportVcfRefNMissing)</span>)) && pc.command_flags1) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10569
</td>
<td class="new_line diff-line-num" data-linenumber="10621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10621
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10621" class="line" lang=""> // special case: just treat the VCF as a .pvar file</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10570
</td>
<td class="new_line diff-line-num" data-linenumber="10622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10622
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10622" class="line" lang=""> strcpy(pvarname, pgenname);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10571
</td>
<td class="new_line diff-line-num" data-linenumber="10623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10623
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10623" class="line" lang=""> pgenname[0] = '\0';</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10609" style="width: 35px; color: rgba(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="10661" style="width: 35px; color: rgba(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">@@ -10609,7 +10661,6 @@ int main(int argc, char** argv) {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10609
</td>
<td class="new_line diff-line-num" data-linenumber="10661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10661
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10661" class="line" lang=""> goto main_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10610
</td>
<td class="new_line diff-line-num" data-linenumber="10662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10662
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10662" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10611
</td>
<td class="new_line diff-line-num" data-linenumber="10663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10663
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10663" class="line" lang=""></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10612
</td>
<td class="new_line diff-line-num old" data-linenumber="10664" style="width: 35px; color: rgba(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="LC10612" class="line" lang=""> // todo: we have to skip this when merging is involved</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10613
</td>
<td class="new_line diff-line-num" data-linenumber="10664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10664
</td>
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<pre style="margin: 0;"> <span id="LC10664" class="line" lang=""> pc.hard_call_thresh = UINT32_MAX;</span>
</pre>
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10614
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<td class="new_line diff-line-num" data-linenumber="10665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10665
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<pre style="margin: 0;"> <span id="LC10665" class="line" lang=""> pc.dosage_erase_thresh = 0;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10615
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<td class="new_line diff-line-num" data-linenumber="10666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10666
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<pre style="margin: 0;"> <span id="LC10666" class="line" lang=""></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10676" style="width: 35px; color: rgba(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="10727" style="width: 35px; color: rgba(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">@@ -10676,19 +10727,11 @@ int main(int argc, char** argv) {</td>
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10676
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<td class="new_line diff-line-num" data-linenumber="10727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10727
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<pre style="margin: 0;"> <span id="LC10727" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10677
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<td class="new_line diff-line-num" data-linenumber="10728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10728
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10728" class="line" lang=""></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10678
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<td class="new_line diff-line-num" data-linenumber="10729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10729
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10729" class="line" lang=""> if (pc.command_flags1 & kfCommand1Pmerge) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10679
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<td class="new_line diff-line-num old" data-linenumber="10730" style="width: 35px; color: rgba(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="LC10679" class="line" lang=""> const uint32_t zst_level = g_zst_level;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10680
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<td class="new_line diff-line-num" data-linenumber="10730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10730
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10730" class="line" lang=""> char* merge_outname_end = outname_end;</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10681
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<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10681" class="line" lang=""> if (pc.command_flags1 == kfCommand1Pmerge) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10682
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<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10682" class="line" lang=""> import_flags |= kfImportKeepAutoconv;</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10683
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<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10683" class="line" lang=""> } else {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10684
</td>
<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10684" class="line" lang=""> if (make_plink2_flags & (kfMakePgen | kfMakePvar | kfMakePsam)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10685
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<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10685" class="line" lang=""> merge_outname_end = strcpya_k(merge_outname_end, "-merge");</span>
</pre>
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10686
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<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10686" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10687
</td>
<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10687" class="line" lang=""> if (!(import_flags & kfImportKeepAutoconv)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10688
</td>
<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10688" class="line" lang=""> g_zst_level = 1;</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10689
</td>
<td class="new_line diff-line-num old" data-linenumber="10731" style="width: 35px; color: rgba(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="LC10689" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="10690" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="10731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10731
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<pre style="margin: 0;">+<span id="LC10731" class="line" lang=""> if (make_plink2_flags & (kfMakePgen | kfMakePvar | kfMakePsam)) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="10690" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="10732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10732
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<pre style="margin: 0;">+<span id="LC10732" class="line" lang=""> merge_outname_end = strcpya_k(merge_outname_end, "-merge");</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10690
</td>
<td class="new_line diff-line-num" data-linenumber="10733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10733
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10733" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="10691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10691
</td>
<td class="new_line diff-line-num old" data-linenumber="10734" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC10691" class="line" lang=""> reterr = Pmerge(&pmerge_info, pc.sample_sort_fname, pc.misc_flags, <span class="idiff left right">import_flags, </span>pc.sample_sort_mode, pc.fam_cols, pc.missing_pheno, pc.max_thread_ct, pc.sort_vars_mode, pgenname, psamname, pvarname, outname, merge_outname_end, &chr_info);</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="10692" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="10734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10734
</td>
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<pre style="margin: 0;">+<span id="LC10734" class="line" lang=""> reterr = Pmerge(&pmerge_info, pc.sample_sort_fname, pc.misc_flags, pc.sample_sort_mode, pc.fam_cols, pc.missing_pheno, pc.max_thread_ct, pc.sort_vars_mode, pgenname, psamname, pvarname, outname, merge_outname_end, &chr_info);</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10692
</td>
<td class="new_line diff-line-num" data-linenumber="10735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10735
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10735" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10693
</td>
<td class="new_line diff-line-num" data-linenumber="10736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10736
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10736" class="line" lang=""> goto main_ret_1;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10694
</td>
<td class="new_line diff-line-num" data-linenumber="10737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10737
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10737" class="line" lang=""> }</span>
</pre>
</td>
</tr>
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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">@@ -10702,10 +10745,9 @@ int main(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC10745" class="line" lang=""> // otherwise error out (since --real-ref-alleles does not make sense on</span>
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10746
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<pre style="margin: 0;"> <span id="LC10746" class="line" lang=""> // the merged .pgen).</span>
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<pre style="margin: 0;"> <span id="LC10747" class="line" lang=""> pc.misc_flags &= ~kfMiscRealRefAlleles;</span>
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<pre style="margin: 0;">-<span id="LC10705" class="line" lang=""> g_zst_level = zst_level;</span>
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10748
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<pre style="margin: 0;"> <span id="LC10748" class="line" lang=""> }</span>
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10749
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<pre style="margin: 0;"> <span id="LC10749" class="line" lang=""></span>
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<pre style="margin: 0;">-<span id="LC10708" class="line" lang=""> if ((pc.command_flags1 & (~(kfCommand1MakePlink2 | kfCommand1Validate | kfCommand1WriteSnplist | kfCommand1WriteCovar | kfCommand1WriteSamples))) || ((pc.command_flags1 & kfCommand1MakePlink2) && (pc.sort_vars_mode <span class="idiff left right">></span> kSortNone))) {</span>
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<pre style="margin: 0;">+<span id="LC10750" class="line" lang=""> if ((pc.command_flags1 & (~(kfCommand1MakePlink2 | kfCommand1Validate | kfCommand1WriteSnplist | kfCommand1WriteCovar | kfCommand1WriteSamples))) || ((pc.command_flags1 & kfCommand1MakePlink2) && (pc.sort_vars_mode <span class="idiff left right"><=</span> kSortNone))) {</span>
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<pre style="margin: 0;"> <span id="LC10751" class="line" lang=""> // split-chromosome prohibited for all commands unless explicitly</span>
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<pre style="margin: 0;"> <span id="LC10752" class="line" lang=""> // permitted here</span>
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<pre style="margin: 0;"> <span id="LC10753" class="line" lang=""> pc.dependency_flags |= kfFilterNoSplitChr;</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">@@ -746,6 +746,15 @@ BoolErr bigstack_calloc_kcp(uintptr_t ct, const char*** kcp_arr_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC746" 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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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_cpp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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;">cpp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpp_arr_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="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</span><span class="p">(</span><span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC751" 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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpp_arr_ptr</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC752" 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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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroPtrArr</span><span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpp_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC755" 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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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"><span class="p">}</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_end_calloc_uc</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ct</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;">uc_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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750
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uc_arr_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="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_end_alloc</span><span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">));</span></span>
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751
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760
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<pre style="margin: 0;"> <span id="LC760" 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="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">uc_arr_ptr</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="1098" style="width: 35px; color: rgba(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="1107" style="width: 35px; color: rgba(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">@@ -1098,7 +1107,6 @@ void BitvecInvertCopy(const uintptr_t* __restrict source_bitvec, uintptr_t word_</td>
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1098
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="cpp"><span class="p">}</span></span>
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp"></span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1102
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BitvecXor</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;">arg_bitvec</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;">main_bitvec</span><span class="p">)</span> <span class="p">{</span></span>
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1103
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// main_bitvec := main_bitvec XOR arg_bitvec</span></span>
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1104
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1112
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<pre style="margin: 0;"> <span id="LC1112" 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 old_line" data-linenumber="1134" style="width: 35px; color: rgba(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="1142" style="width: 35px; color: rgba(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">@@ -1134,7 +1142,6 @@ void BitvecXor(const uintptr_t* __restrict arg_bitvec, uintptr_t word_ct, uintpt</td>
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1134
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="p">}</span></span>
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1135
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1136
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"><span class="p">}</span></span>
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1137
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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1138
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1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp"></span>
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1139
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BitvecInvertAndMask</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;">include_bitvec</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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">main_bitvec</span><span class="p">)</span> <span class="p">{</span></span>
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1140
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// main_bitvec := (~main_bitvec) AND include_bitvec</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">@@ -604,6 +604,11 @@ HEADER_INLINE BoolErr bigstack_alloc_wpp(uintptr_t ct, uintptr_t**** wpp_arr_ptr</td>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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;">wpp_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC607" 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;">bigstack_alloc_cpp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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;">cpp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cpp_arr_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="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</span><span class="p">(</span><span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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;">cpp_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC612" 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;">bigstack_alloc_u32pp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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;">u32pp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u32pp_arr_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="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;">bigstack_alloc</span><span class="p">(</span><span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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;">u32pp_arr_ptr</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">@@ -636,6 +641,8 @@ BoolErr bigstack_calloc_cp(uintptr_t ct, char*** cp_arr_ptr);</td>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_kcp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ct</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;">kcp_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_cpp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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;">cpp_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC646" 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;">bigstack_calloc_c</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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;">c_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bigstack_calloc_uc</span><span class="p">(</span><span class="n" style="color: #333;">ct</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;">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;">c_arr_ptr</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"><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">@@ -1177,7 +1184,7 @@ HEADER_INLINE void AlignedBitarrInvertCopy(const uintptr_t* __restrict source_bi</td>
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1177
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp"> <span class="p">}</span></span>
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1178
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp"><span class="p">}</span></span>
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1179
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="cpp"></span>
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1180
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<pre style="margin: 0;">-<span id="LC1180" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>void BitvecXor(const uintptr_t* __restrict arg_bitvec, uintptr_t word_ct, uintptr_t* main_bitvec);</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BitvecXor</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;">arg_bitvec</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;">main_bitvec</span><span class="p">);</span></span>
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1181
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="cpp"></span>
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1182
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BitvecInvertAndMask</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;">include_bitvec</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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">main_bitvec</span><span class="p">);</span></span>
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1183
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -171,19 +171,21 @@ FLAGSET64_DEF_START()</td>
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfLgenRef</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;">25</span><span class="p">),</span></span>
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172
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfList</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;">26</span><span class="p">),</span></span>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfRlist</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;">27</span><span class="p">),</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfOxGen</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;">28</span><span class="p">),</span></span>
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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;">kfExportfPed</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;">29</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="n" style="color: #333;">kfExportfCompound</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;">30</span><span class="p">),</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfStructure</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1U</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">31</span><span class="p">),</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfTranspose</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">32</span><span class="p">),</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfVcf42</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">33</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="n" style="color: #333;">kfExportfVcf43</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">34</span><span class="p">),</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfOxGenV1</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;">28</span><span class="p">),</span></span>
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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;">kfExportfOxGenV2</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;">29</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="n" style="color: #333;">kfExportfOxGen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kfExportfOxGenV1</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfExportfOxGenV2</span><span class="p">,</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfPed</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;">30</span><span class="p">),</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfCompound</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1U</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">31</span><span class="p">),</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfStructure</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">32</span><span class="p">),</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfTranspose</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">33</span><span class="p">),</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfVcf42</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">34</span><span class="p">),</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfVcf43</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">35</span><span class="p">),</span></span>
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181
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfVcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kfExportfVcf42</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfExportfVcf43</span><span class="p">,</span></span>
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182
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfTypemask</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">2LLU</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kfExportfVcf43</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfExportf23</span><span class="p">,</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfIncludeAlt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">5</span></span><span class="p">),</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfBgz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">6</span></span><span class="p">),</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfOmitNonmaleY</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">7</span></span><span class="p">),</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfSampleV2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">8</span></span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfIncludeAlt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">6</span></span><span class="p">),</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfBgz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">7</span></span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfOmitNonmaleY</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">8</span></span><span class="p">),</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">kfExportfSampleV2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1LLU</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3<span class="idiff left right">9</span></span><span class="p">)</span></span>
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187
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET64_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">ExportfFlags</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_START</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">@@ -389,7 +391,7 @@ void PopulateRescaledDosageF(const uintptr_t* genoarr, const uintptr_t* dosage_p</td>
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"></span>
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392
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<pre style="margin: 0;"> <span id="LC392" 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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391
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393
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<pre style="margin: 0;"> <span id="LC393" 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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392
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<pre style="margin: 0;">-<span id="LC392" 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;"><span class="idiff left">DivUp</span></span><span class="p"><span class="idiff">(</span></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 right">kBitsPerWordD2</span></span><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="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;"><span class="idiff left">NypCtToWordCt</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">sample_ct</span></span><span class="p">);</span></span>
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393
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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;">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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394
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396
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<pre style="margin: 0;"> <span id="LC396" 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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395
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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;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -174,7 +174,7 @@ void PvarInfoWrite(uint32_t info_pr_flag_present, uint32_t is_pr, char* info_tok</td>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">info_token</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;"> <span id="LC175" 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;">info_token_pr</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="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">info_token_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">PrInInfoToken</span></span><span class="p">(</span><span class="n" style="color: #333;">info_token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">info_token</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">info_token_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">InfoPrStart</span></span><span class="p">(</span><span class="n" style="color: #333;">info_token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">info_token</span><span class="p">);</span></span>
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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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<pre style="margin: 0;"> <span id="LC179" 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="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="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_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_token_pr</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">@@ -553,14 +553,20 @@ PglErr WritePvar(const char* outname, const uintptr_t* variant_include, const Ch</td>
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<pre style="margin: 0;"> <span id="LC553" 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_variant_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;">raw_variant_ct</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC554" 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;">all_nonref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nonref_flags_storage</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="LC555" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_nonref</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_info_reload</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;">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="p">{</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;">// bugfix (6 Feb 2021): don't write INFO column when INFO column</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// explicitly excluded here, but pvar_info_reload is needed for some</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// other reason</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_info_reload</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="LC561" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC562" 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;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC563" 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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nonref_flags</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</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;">nonref_flags</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">write_info</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC567" 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;">write_info_pr</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;">kfInfoPrNonflagPresent</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC568" 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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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"><span class="idiff left">'</span>provisional reference<span class="idiff right">'</span> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n<span class="idiff left">\"</span></span><span class="s" style="color: #d14;">provisional reference</span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;"> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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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564
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvar_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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565
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"> <span class="p">}</span></span>
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566
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1190" style="width: 35px; color: rgba(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">@@ -1184,9 +1190,9 @@ PglErr WritePsam(const char* outname, const uintptr_t* sample_include, const Sam</td>
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1184
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="old_line diff-line-num" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1186
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<td class="new_line diff-line-num" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#ifdef NO_UNALIGNED</span></span>
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1187
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<td class="new_line diff-line-num old" data-linenumber="1193" style="width: 35px; color: rgba(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="LC1187" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"># error "Unaligned accesses in Bitvec<span class="idiff left right">Resort</span>()."</span></span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"># error "Unaligned accesses in Bitvec<span class="idiff left right">Permute</span>()."</span></span>
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1188
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1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#endif</span></span>
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1189
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">void Bitvec<span class="idiff left right">Resort</span>(const uintptr_t* bitvec, const uint32_t* new_sample_idx_to_old, uint32_t sample_ct, unsigned char* writebuf) {</span></span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">void Bitvec<span class="idiff left right">Permute</span>(const uintptr_t* bitvec, const uint32_t* new_sample_idx_to_old, uint32_t sample_ct, unsigned char* writebuf) {</span></span>
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1190
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t sample_ctl_m1 = BitCtToWordCt(sample_ct) - 1;</span></span>
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1191
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t widx = 0;</span></span>
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1192
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t cur_word_entry_ct = kBitsPerWord;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1210" style="width: 35px; color: rgba(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="1216" style="width: 35px; color: rgba(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">@@ -1210,37 +1216,111 @@ void BitvecResort(const uintptr_t* bitvec, const uint32_t* new_sample_idx_to_old</td>
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1210
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">}</span></span>
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1211
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<td class="new_line diff-line-num" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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1212
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Now assumes trailing bits of genovec have been zeroed out.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// writebuf need not be word-aligned.</span></span>
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1213
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NO_UNALIGNED</span></span>
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1214
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<pre style="margin: 0;">-<span id="LC1214" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># error "Unaligned accesses in Genovec<span class="idiff left right">Resort</span>()."</span></span>
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1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># error "Unaligned accesses in Genovec<span class="idiff left right">Permute</span>()."</span></span>
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1215
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1223
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<pre style="margin: 0;"> <span id="LC1223" 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="LC1216" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Genovec<span class="idiff left">Resort</span></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;">genovec</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;"><span class="idiff">new</span>_sample_idx_to_<span class="idiff right">old</span></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;">writebuf</span><span class="p">)</span> <span class="p">{</span></span>
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1217
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<pre style="margin: 0;">-<span id="LC1217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// writebuf need not be word-aligned</span></span></span>
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1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Genovec<span class="idiff left">Permute</span></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;">genovec</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;"><span class="idiff">old</span>_sample_idx_to_<span class="idiff right">new</span></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;">writebuf</span><span class="p">)</span> <span class="p">{</span></span>
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1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">most_common_geno_word</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">MostCommonGenoUnsafe</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">genovec</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="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kMask5555</span></span><span class="p"><span class="idiff right">;</span></span></span>
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1226
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<pre style="margin: 0;"> <span id="LC1226" 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="n" style="color: #333;">NypCtToWordCt</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1219
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<pre style="margin: 0;">-<span id="LC1219" 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;">new_sample_idx_to_old_iter</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>
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1220
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1227
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<pre style="margin: 0;"> <span id="LC1227" 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;">writebuf_walias</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;">writebuf</span><span class="p">);</span></span>
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1221
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1228
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<pre style="margin: 0;"> <span id="LC1228" 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="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="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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1222
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<pre style="margin: 0;">-<span id="LC1222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_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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1223
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<pre style="margin: 0;">-<span id="LC1223" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this is noticeably better than the ascending loop</span></span>
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1224
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<pre style="margin: 0;">-<span id="LC1224" 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="n" style="color: #333;">kBitsPerWordD2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="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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1225
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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_word</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">GetNyparrEntry</span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">new_sample_idx_to_old_iter</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">]);</span></span>
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1226
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<pre style="margin: 0;">-<span id="LC1226" 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;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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1227
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<pre style="margin: 0;">-<span id="LC1227" 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="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">most_common_geno_word</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="cpp"> <span class="p">}</span></span>
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1231
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<pre style="margin: 0;">+<span id="LC1231" 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;">trailing_bit_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="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>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">SubwordStore</span><span class="p">(</span><span class="n" style="color: #333;">bzhi_max</span><span class="p">(</span><span class="n" style="color: #333;">most_common_geno_word</span><span class="p">,</span> <span class="n" style="color: #333;">trailing_bit_ct</span><span class="p">),</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">trailing_bit_ct</span><span class="p">,</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">]));</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"></span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" 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;">writebuf_b</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;">writebuf</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1235
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<pre style="margin: 0;">+<span id="LC1235" 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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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word_xor</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" 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="new_line diff-line-num new" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" 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="new_line diff-line-num new" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1228
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"> <span class="p">}</span></span>
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1229
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<td class="new_line diff-line-num old" data-linenumber="1241" style="width: 35px; color: rgba(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="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_word</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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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bzhi_max</span><span class="p">(</span><span class="n" style="color: #333;">most_common_geno_word</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">genovec</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">],</span> <span class="n" style="color: #333;">trailing_bit_ct</span><span class="p">);</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" 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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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">most_common_geno_word</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">genovec</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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1230
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp"> <span class="p">}</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_word</span><span class="p">;</span></span>
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1232
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<td class="new_line diff-line-num old" data-linenumber="1245" style="width: 35px; color: rgba(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="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">new_sample_idx_to_old_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;">new_sample_idx_to_old_iter</span><span class="p">[</span><span class="n" style="color: #333;">kBitsPerWordD2</span><span class="p">]);</span></span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" 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;">geno_word_xor</span><span class="p">)</span> <span class="p">{</span></span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="p">}</span></span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" 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;">cur_old_sample_idx_to_new</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;">old_sample_idx_to_new</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;">kBitsPerWordD2</span><span class="p">]);</span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" 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;">bit_read_shift_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kBitsPerWord</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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1251
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<pre style="margin: 0;">+<span id="LC1251" 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_geno_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">bit_read_shift_ct</span><span class="p">)</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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1252
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<pre style="margin: 0;">+<span id="LC1252" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">bit_read_shift_ct</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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1253
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<pre style="margin: 0;">+<span id="LC1253" 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;">new_byte_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</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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1254
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<pre style="margin: 0;">+<span id="LC1254" 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;">bit_write_shift_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;">new_sample_idx</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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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Value has been preset to most_common_geno, so if we xor it with</span></span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (most_common_geno ^ actual_geno), the result is actual_geno.</span></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;">writebuf_b</span><span class="p">[</span><span class="n" style="color: #333;">new_byte_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">cur_geno_xor</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bit_write_shift_ct</span><span class="p">;</span></span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</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="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k1LU</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bit_read_shift_ct</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 class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span><span class="p">);</span></span>
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1233
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1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="cpp"> <span class="p">}</span></span>
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1234
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<pre style="margin: 0;">-<span id="LC1234" 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_word_entry_ct</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>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_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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1236
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<pre style="margin: 0;">-<span id="LC1236" 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="n" style="color: #333;">cur_word_entry_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="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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1237
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<pre style="margin: 0;">-<span id="LC1237" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_word</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">GetNyparrEntry</span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">new_sample_idx_to_old_iter</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">]);</span></span>
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1238
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<pre style="margin: 0;">-<span id="LC1238" 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;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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1239
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<pre style="margin: 0;">-<span id="LC1239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"><span class="p">}</span></span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GenovecPermuteSubset</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;">genovec</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="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_interleaved_vec</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;">old_sample_idx_to_new</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;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">writebuf</span><span class="p">)</span> <span class="p">{</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" 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="n" style="color: #333;">raw_sample_ct</span><span class="p">)</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;">GenovecPermute</span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">writebuf</span><span class="p">);</span></span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="cpp"> <span class="p">}</span></span>
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1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"> <span class="n" style="color: #333;">STD_ARRAY_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">genocounts</span><span class="p">);</span></span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp"> <span class="n" style="color: #333;">GenoarrCountSubsetFreqs</span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include_interleaved_vec</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;">genocounts</span><span class="p">);</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">most_common_geno</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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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">most_common_geno_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="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1273
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<pre style="margin: 0;">+<span id="LC1273" 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;">cur_geno</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;">cur_geno</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;">cur_geno</span><span class="p">)</span> <span class="p">{</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="n" style="color: #333;">cur_geno</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">most_common_geno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_geno</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="n" style="color: #333;">cur_geno</span><span class="p">];</span></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="p">}</span></span>
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1240
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <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;">cur_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_word</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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1242
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="p">}</span></span>
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1243
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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">SubwordStore</span><span class="p">(</span><span class="n" style="color: #333;">cur_word</span><span class="p">,</span> <span class="n" style="color: #333;">NypCtToByteCt</span><span class="p">(</span><span class="n" style="color: #333;">cur_word_entry_ct</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">]));</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" 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;">most_common_geno_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">most_common_geno</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kMask5555</span><span class="p">;</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" 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="n" style="color: #333;">NypCtToWordCt</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" 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;">writebuf_walias</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;">writebuf</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" 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="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="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="new_line diff-line-num new" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">most_common_geno_word</span><span class="p">;</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="p">}</span></span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" 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;">write_trailing_bit_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="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>
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<td class="new_line diff-line-num new" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">SubwordStore</span><span class="p">(</span><span class="n" style="color: #333;">bzhi_max</span><span class="p">(</span><span class="n" style="color: #333;">most_common_geno_word</span><span class="p">,</span> <span class="n" style="color: #333;">write_trailing_bit_ct</span><span class="p">),</span> <span class="n" style="color: #333;">DivUp</span><span class="p">(</span><span class="n" style="color: #333;">write_trailing_bit_ct</span><span class="p">,</span> <span class="n" style="color: #333;">CHAR_BIT</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">writebuf_walias</span><span class="p">[</span><span class="n" style="color: #333;">sample_ctl2_m1</span><span class="p">]));</span></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">most_common_geno_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"> <span class="p">}</span></span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"></span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" 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_ctl2_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NypCtToWordCt</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" 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;">sample_include_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;">sample_include</span><span class="p">);</span></span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" 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;">writebuf_b</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;">writebuf</span><span class="p">);</span></span>
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1295
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<pre style="margin: 0;">+<span id="LC1295" 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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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">geno_word_xor</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1297
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<pre style="margin: 0;">+<span id="LC1297" 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;">raw_sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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1298
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<pre style="margin: 0;">+<span id="LC1298" 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;">raw_sample_ctl2_m1</span><span class="p">)</span> <span class="p">{</span></span>
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1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"> <span class="p">}</span></span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bzhi_max</span><span class="p">(</span><span class="n" style="color: #333;">most_common_geno_word</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">genovec</span><span class="p">[</span><span class="n" style="color: #333;">widx</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;">ModNz</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;">kBitsPerWordD2</span><span class="p">));</span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" 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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1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">most_common_geno_word</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">genovec</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">];</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="cpp"> <span class="p">}</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" 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;">geno_word_xor</span><span class="p">)</span> <span class="p">{</span></span>
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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp"> <span class="p">}</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">&=</span> <span class="n" style="color: #333;">UnpackHalfwordToWord</span><span class="p">(</span><span class="n" style="color: #333;">sample_include_alias</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">])</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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1309
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<pre style="margin: 0;">+<span id="LC1309" 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;">geno_word_xor</span><span class="p">)</span> <span class="p">{</span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"> <span class="p">}</span></span>
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1312
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<pre style="margin: 0;">+<span id="LC1312" 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;">cur_old_sample_idx_to_new</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;">old_sample_idx_to_new</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;">kBitsPerWordD2</span><span class="p">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" 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;">bit_read_shift_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kBitsPerWord</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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1315
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<pre style="margin: 0;">+<span id="LC1315" 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_geno_xor</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">bit_read_shift_ct</span><span class="p">)</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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1316
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<pre style="margin: 0;">+<span id="LC1316" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">bit_read_shift_ct</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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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assert(new_sample_idx != UINT32_MAX);</span></span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" 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;">new_byte_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</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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1319
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<pre style="margin: 0;">+<span id="LC1319" 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;">bit_write_shift_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;">new_sample_idx</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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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_b</span><span class="p">[</span><span class="n" style="color: #333;">new_byte_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">^=</span> <span class="n" style="color: #333;">cur_geno_xor</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bit_write_shift_ct</span><span class="p">;</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_word_xor</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="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">k1LU</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bit_read_shift_ct</span><span class="p">;</span></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">geno_word_xor</span><span class="p">);</span></span>
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1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="cpp"> <span class="p">}</span></span>
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"><span class="p">}</span></span>
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1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"></span>
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Revised phaseraw:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1292" style="width: 35px; color: rgba(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="1372" style="width: 35px; color: rgba(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">@@ -1292,7 +1372,7 @@ void UnpackHphaseSubset(const uintptr_t* __restrict all_hets, const uintptr_t* _</td>
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="cpp"> <span class="p">}</span></span>
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1293
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1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="cpp"><span class="p">}</span></span>
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1294
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1374
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<pre style="margin: 0;"> <span id="LC1374" class="line" lang="cpp"></span>
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1295
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<pre style="margin: 0;">-<span id="LC1295" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UnpackAnd<span class="idiff left right">Resort</span>Hphase</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;">all_hets</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;">phaseraw</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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">uintptr_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">phasepresent_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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">)</span> <span class="p">{</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UnpackAnd<span class="idiff left right">Permute</span>Hphase</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;">all_hets</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;">phaseraw</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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">uintptr_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">phasepresent_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="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">phaseinfo</span><span class="p">)</span> <span class="p">{</span></span>
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1296
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1376
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<pre style="margin: 0;"> <span id="LC1376" 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;">aux2a_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;">phaseraw</span><span class="p">[</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kBytesPerWord</span><span class="p">]);</span></span>
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1297
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1377
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<pre style="margin: 0;"> <span id="LC1377" 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;">old_sample_idx_to_new_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">;</span></span>
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1298
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1378
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<pre style="margin: 0;"> <span id="LC1378" 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_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;">raw_sample_ct</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1509" style="width: 35px; color: rgba(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="1589" style="width: 35px; color: rgba(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">@@ -1509,44 +1589,122 @@ void CopyDosage(const uintptr_t* __restrict read_dosagepresent, const Dosage* re</td>
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1509
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1589
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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">write_dosagevals</span><span class="p">,</span> <span class="n" style="color: #333;">read_dosagevals</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Dosage</span><span class="p">));</span></span>
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1510
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1590
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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="cpp"><span class="p">}</span></span>
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1511
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1591
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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1512
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<pre style="margin: 0;">-<span id="LC1512" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndResort8bit</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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">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;">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;">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 class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">cumulative_popcount_buf</span><span class="p">)</span> <span class="p">{</span></span>
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1513
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<pre style="margin: 0;">-<span id="LC1513" 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_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;">raw_sample_ct</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1514
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<pre style="margin: 0;">-<span id="LC1514" class="line" lang="cpp"> <span class="n" style="color: #333;">FillCumulativePopcounts</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">cumulative_popcount_buf</span><span class="p">);</span></span>
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1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndPermute8bit</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="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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">val_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 class="p">{</span></span>
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1515
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<td class="new_line diff-line-num" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1593
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<pre style="margin: 0;"> <span id="LC1593" 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_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;">sample_ct</span><span class="p">);</span></span>
</pre>
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1516
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1594
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<pre style="margin: 0;"> <span id="LC1594" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1517
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1595
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<pre style="margin: 0;"> <span id="LC1595" 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;">src_vals_uc</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;">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;">src_vals</span><span class="p">);</span></span>
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1518
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1596
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<pre style="margin: 0;"> <span id="LC1596" 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;">dst_vals_uc</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;">dst_vals</span><span class="p">);</span></span>
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1519
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<td class="new_line diff-line-num old" data-linenumber="1597" style="width: 35px; color: rgba(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="LC1519" 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;">dst_vals_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_vals_uc</span><span class="p">;</span></span>
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1520
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<pre style="margin: 0;">-<span id="LC1520" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Tried word-based loop, was significantly worse</span></span>
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1521
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<pre style="margin: 0;">-<span id="LC1521" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1522
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<pre style="margin: 0;">-<span id="LC1522" 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_sample_idx</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="n" style="color: #333;">new_sample_idx</span><span class="p">];</span></span>
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1523
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<pre style="margin: 0;">-<span id="LC1523" 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;">src_subset</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx</span><span class="p">))</span> <span class="p">{</span></span>
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1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="cpp"></span>
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1598
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<pre style="margin: 0;">+<span id="LC1598" 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="n" style="color: #333;">src_subset</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_val_ct</span><span class="p">;</span></span>
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1600
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<pre style="margin: 0;">+<span id="LC1600" 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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1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">old_sample_idx_base</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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1602
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<pre style="margin: 0;">+<span id="LC1602" 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;">old_val_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;">old_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1603
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<pre style="margin: 0;">+<span id="LC1603" 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_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">old_sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1604
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<pre style="margin: 0;">+<span id="LC1604" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">old_sample_idx</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="cpp"> <span class="n" style="color: #333;">dst_vals_uc</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_vals_uc</span><span class="p">[</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">];</span></span>
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1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="cpp"> <span class="p">}</span></span>
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1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="cpp"> <span class="n" style="color: #333;">new_val_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" 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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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_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>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="cpp"> <span class="n" style="color: #333;">new_val_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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1612
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<pre style="margin: 0;">+<span id="LC1612" 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;">old_val_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;">old_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1613
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<pre style="margin: 0;">+<span id="LC1613" 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;">old_sample_idx_lowbit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1y</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1614
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<pre style="margin: 0;">+<span id="LC1614" 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;">sample_include</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">old_sample_idx_lowbit</span><span class="p">))</span> <span class="p">{</span></span>
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1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="cpp"> <span class="p">}</span></span>
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1617
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<pre style="margin: 0;">+<span id="LC1617" 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_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kBitsPerWord</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">old_sample_idx_lowbit</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1618
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<pre style="margin: 0;">+<span id="LC1618" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">old_sample_idx</span><span class="p">];</span></span>
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1524
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1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1525
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<pre style="margin: 0;">-<span id="LC1525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">old_dosagevals</span>_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">RawToSubsettedPos</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">src_subset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cumulative_popcount_buf</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">old_sample</span>_idx</span><span class="p"><span class="idiff right">)</span>;</span></span>
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1526
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<pre style="margin: 0;">-<span id="LC1526" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">dst_vals_iter</span></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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">src_vals_uc</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">old_dosagevals_idx</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dst_vals_uc</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">new_sample</span>_idx</span><span class="p"><span class="idiff">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">src_vals_uc</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">old_val</span>_idx</span><span class="p"><span class="idiff right">]</span>;</span></span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">++</span></span><span class="n" style="color: #333;"><span class="idiff right">new_val_ct</span></span><span class="p">;</span></span>
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1527
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="cpp"> <span class="p">}</span></span>
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1528
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1623
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<pre style="margin: 0;"> <span id="LC1623" class="line" lang="cpp"> <span class="p">}</span></span>
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1529
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<pre style="margin: 0;">-<span id="LC1529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dst_vals_iter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dst_vals_uc</span><span class="p">;</span></span>
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1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">new_sample_idx_base</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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1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1626
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<pre style="margin: 0;">+<span id="LC1626" 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_val_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;">new_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">new_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1627" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">dst_subset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">new_sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="cpp"> <span class="n" style="color: #333;">dst_vals_uc</span><span class="p">[</span><span class="n" style="color: #333;">new_val_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_vals_uc</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_val_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="cpp"><span class="p">}</span></span>
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1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1532" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndResort16bit</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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">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;">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;">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 class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">cumulative_popcount_buf</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1533" 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_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;">raw_sample_ct</span><span class="p">);</span></span>
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1534
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<pre style="margin: 0;">-<span id="LC1534" class="line" lang="cpp"> <span class="n" style="color: #333;">FillCumulativePopcounts</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">cumulative_popcount_buf</span><span class="p">);</span></span>
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1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndPermute16bit</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="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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">val_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 class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1634" 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_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;">sample_ct</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1537
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <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;">src_vals_u16</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;">uint16_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">src_vals</span><span class="p">);</span></span>
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1538
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<pre style="margin: 0;"> <span id="LC1637" 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;">dst_vals_u16</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;">dst_vals</span><span class="p">);</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;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dst_vals_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_vals_u16</span><span class="p">;</span></span>
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1540
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<pre style="margin: 0;">-<span id="LC1540" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Tried word-based loop, was significantly worse</span></span>
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1541
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<pre style="margin: 0;">-<span id="LC1541" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1542" 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_sample_idx</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="n" style="color: #333;">new_sample_idx</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="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;">src_subset</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="cpp"></span>
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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;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_subset</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_val_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1641" 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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1642
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">old_sample_idx_base</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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1643
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<pre style="margin: 0;">+<span id="LC1643" 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;">old_val_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;">old_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1644
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<pre style="margin: 0;">+<span id="LC1644" 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_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">old_sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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1645
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<pre style="margin: 0;">+<span id="LC1645" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">old_sample_idx</span><span class="p">];</span></span>
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1646
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<pre style="margin: 0;">+<span id="LC1646" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1647
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="cpp"> <span class="n" style="color: #333;">dst_vals_u16</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_vals_u16</span><span class="p">[</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">];</span></span>
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1648
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<pre style="margin: 0;">+<span id="LC1648" class="line" lang="cpp"> <span class="p">}</span></span>
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1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="cpp"> <span class="n" style="color: #333;">new_val_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span></span>
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1650
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<pre style="margin: 0;">+<span id="LC1650" 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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1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_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>
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1652
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<pre style="margin: 0;">+<span id="LC1652" class="line" lang="cpp"> <span class="n" style="color: #333;">new_val_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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1653
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<pre style="margin: 0;">+<span id="LC1653" 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;">old_val_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;">old_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">old_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1654" 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;">old_sample_idx_lowbit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1y</span><span class="p">(</span><span class="n" style="color: #333;">src_subset</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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1655
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<pre style="margin: 0;">+<span id="LC1655" 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;">sample_include</span><span class="p">[</span><span class="n" style="color: #333;">widx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">old_sample_idx_lowbit</span><span class="p">))</span> <span class="p">{</span></span>
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1656
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<pre style="margin: 0;">+<span id="LC1656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="cpp"> <span class="p">}</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" 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_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kBitsPerWord</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">old_sample_idx_lowbit</span><span class="p">);</span></span>
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1659
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<pre style="margin: 0;">+<span id="LC1659" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">old_sample_idx</span><span class="p">];</span></span>
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1544
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">);</span></span>
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1545
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<pre style="margin: 0;">-<span id="LC1545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">old_dosagevals</span>_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">RawToSubsettedPos</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">src_subset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cumulative_popcount_buf</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">old_sample</span>_idx</span><span class="p"><span class="idiff right">)</span>;</span></span>
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1546
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<pre style="margin: 0;">-<span id="LC1546" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">dst_vals_iter</span></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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">src_vals_u16</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">old_dosagevals_idx</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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1661
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<pre style="margin: 0;">+<span id="LC1661" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">dst_vals_u16</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">new_sample</span>_idx</span><span class="p"><span class="idiff">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">src_vals_u16</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">old_val</span>_idx</span><span class="p"><span class="idiff right">]</span>;</span></span>
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1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">++</span></span><span class="n" style="color: #333;"><span class="idiff right">new_val_ct</span></span><span class="p">;</span></span>
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1547
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="cpp"> <span class="p">}</span></span>
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1548
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1664
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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp"> <span class="p">}</span></span>
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1549
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<pre style="margin: 0;">-<span id="LC1549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dst_vals_iter</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dst_vals_u16</span><span class="p">;</span></span>
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1665
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<pre style="margin: 0;">+<span id="LC1665" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">new_sample_idx_base</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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1666
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<pre style="margin: 0;">+<span id="LC1666" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_subset</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><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="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_val_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;">new_val_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_val_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">new_val_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1668
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<pre style="margin: 0;">+<span id="LC1668" 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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">dst_subset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">new_sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="cpp"> <span class="n" style="color: #333;">dst_vals_u16</span><span class="p">[</span><span class="n" style="color: #333;">new_val_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_vals_u16</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_val_ct</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="p">}</span></span>
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1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="cpp"></span>
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1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Dense8bitToSparse</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;">set</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ctl</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;">vals</span><span class="p">)</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="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;">vals_uc</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;">vals</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="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1677
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<pre style="margin: 0;">+<span id="LC1677" 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="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</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="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">set_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">set</span><span class="p">[</span><span class="n" style="color: #333;">widx</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;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">set_word</span><span class="p">)</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;">continue</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="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="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;">cur_vals_read</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;">vals_uc</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;">kBitsPerWord</span><span class="p">]);</span></span>
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1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</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="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_idx_lowbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">set_word</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;">vals_uc</span><span class="p">[</span><span class="n" style="color: #333;">write_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_vals_read</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx_lowbits</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="n" style="color: #333;">set_word</span> <span class="o" style="font-weight: 600;">&=</span> <span class="n" style="color: #333;">set_word</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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1687
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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">set_word</span><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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write_idx</span><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>
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1692
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<pre style="margin: 0;">+<span id="LC1692" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Dense16bitToSparse</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;">set</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ctl</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;">vals</span><span class="p">)</span> <span class="p">{</span></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;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vals_u16</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;">vals</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;">uint32_t</span> <span class="n" style="color: #333;">write_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1695
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<pre style="margin: 0;">+<span id="LC1695" 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="n" style="color: #333;">widx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">widx</span><span class="p">)</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="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">set_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">set</span><span class="p">[</span><span class="n" style="color: #333;">widx</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="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;">set_word</span><span class="p">)</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="k" style="font-weight: 600;">continue</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="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="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_vals_read</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;">vals_u16</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;">kBitsPerWord</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;">do</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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx_lowbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctzw</span><span class="p">(</span><span class="n" style="color: #333;">set_word</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="n" style="color: #333;">vals_u16</span><span class="p">[</span><span class="n" style="color: #333;">write_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_vals_read</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx_lowbits</span><span class="p">];</span></span>
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1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="cpp"> <span class="n" style="color: #333;">set_word</span> <span class="o" style="font-weight: 600;">&=</span> <span class="n" style="color: #333;">set_word</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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1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">set_word</span><span class="p">);</span></span>
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1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="cpp"> <span class="p">}</span></span>
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1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write_idx</span><span class="p">;</span></span>
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1550
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="cpp"><span class="p">}</span></span>
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1551
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1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="cpp"></span>
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1552
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1710
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<pre style="margin: 0;"> <span id="LC1710" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Requires trailing bits of genovec to be zeroed out.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3517" style="width: 35px; color: rgba(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="3675" style="width: 35px; color: rgba(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">@@ -3517,13 +3675,13 @@ BoolErr FillInfoVtypeNum(const char* num_str_start, int32_t* info_vtype_num_ptr)</td>
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3517
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3675
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<pre style="margin: 0;"> <span id="LC3675" 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_num_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="3518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3518
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3676
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<pre style="margin: 0;"> <span id="LC3676" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_vtype_num_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kInfoVtypeR</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3519
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<td class="new_line diff-line-num" data-linenumber="3677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3677
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<pre style="margin: 0;"> <span id="LC3677" 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;">likely</span><span class="p">(</span><span class="n" style="color: #333;">first_num_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3520
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<pre style="margin: 0;">-<span id="LC3520" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_vtype_num_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kInfoVtype<span class="idiff left right">G</span></span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3521" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="3678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3678
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<pre style="margin: 0;">+<span id="LC3678" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_vtype_num_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kInfoVtype<span class="idiff left right">Unknown</span></span><span class="p">;</span></span>
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3521
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<td class="new_line diff-line-num" data-linenumber="3679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3679
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<pre style="margin: 0;"> <span id="LC3679" 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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3522
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3680
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<pre style="margin: 0;"> <span id="LC3680" 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="old_line diff-line-num" data-linenumber="3523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3523
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3681
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<pre style="margin: 0;"> <span id="LC3681" class="line" lang="cpp"> <span class="p">}</span></span>
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3524
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<td class="new_line diff-line-num" data-linenumber="3682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3682
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<pre style="margin: 0;"> <span id="LC3682" 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="old_line diff-line-num" data-linenumber="3525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3525
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3683
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<pre style="margin: 0;"> <span id="LC3683" 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="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3526
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<td class="new_line diff-line-num old" data-linenumber="3684" style="width: 35px; color: rgba(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="LC3526" 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;">ScanmovPosintCapped</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">UINT32_MAX</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">num_str_start</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">num_str_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="old_line diff-line-num new" data-linenumber="3527" style="width: 35px; color: rgba(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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3684
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<pre style="margin: 0;">+<span id="LC3684" 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;">ScanmovPosintCapped</span><span class="p">(</span><span class="mh" style="color: #099;"><span class="idiff left right">0x3fffffff</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">num_str_start</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">num_str_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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3527
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3685
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<pre style="margin: 0;"> <span id="LC3685" 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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3528
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3686
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<pre style="margin: 0;"> <span id="LC3686" class="line" lang="cpp"> <span class="p">}</span></span>
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3529
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3687
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<pre style="margin: 0;"> <span id="LC3687" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_vtype_num_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3681" style="width: 35px; color: rgba(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="3839" style="width: 35px; color: rgba(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">@@ -3681,14 +3839,17 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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3681
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3839
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<pre style="margin: 0;"> <span id="LC3839" 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_variant_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;">raw_variant_ct</span><span class="p">);</span></span>
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3682
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3840
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<pre style="margin: 0;"> <span id="LC3840" 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;">all_nonref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nonref_flags_storage</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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3683
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3841
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<pre style="margin: 0;"> <span id="LC3841" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_nonref</span><span class="p">;</span></span>
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3684
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<pre style="margin: 0;">-<span id="LC3684" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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3842
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<pre style="margin: 0;">+<span id="LC3842" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_info_reload</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;">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="p">{</span></span>
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3843
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<pre style="margin: 0;">+<span id="LC3843" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_info_reload</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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3844
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<pre style="margin: 0;">+<span id="LC3844" class="line" lang="cpp"> <span class="p">}</span></span>
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3845
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<pre style="margin: 0;">+<span id="LC3845" 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;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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3685
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3846
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<pre style="margin: 0;"> <span id="LC3846" 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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nonref_flags</span><span class="p">)</span> <span class="p">{</span></span>
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3686
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3847
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<pre style="margin: 0;"> <span id="LC3847" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</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;">nonref_flags</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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3687
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3848
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<pre style="margin: 0;"> <span id="LC3848" class="line" lang="cpp"> <span class="p">}</span></span>
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3688
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<td class="new_line diff-line-num" data-linenumber="3849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3849
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<pre style="margin: 0;"> <span id="LC3849" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">write_info</span><span class="p">;</span></span>
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3689
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3850
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<pre style="margin: 0;"> <span id="LC3850" 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;">write_info_pr</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;">kfInfoPrNonflagPresent</span><span class="p">)))</span> <span class="p">{</span></span>
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3690
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3851
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<pre style="margin: 0;"> <span id="LC3851" 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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<td class="old_line diff-line-num old" data-linenumber="3691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3691
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<td class="new_line diff-line-num old" data-linenumber="3852" style="width: 35px; color: rgba(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="LC3691" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"><span class="idiff left">'</span>provisional reference<span class="idiff right">'</span> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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="new_line diff-line-num new" data-linenumber="3852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3852
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<pre style="margin: 0;">+<span id="LC3852" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n<span class="idiff left">\"</span></span><span class="s" style="color: #d14;">provisional reference</span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;"> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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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3692
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3853
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<pre style="margin: 0;"> <span id="LC3853" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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3693
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3854
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<pre style="margin: 0;"> <span id="LC3854" class="line" lang="cpp"> <span class="p">}</span></span>
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3694
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3855
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<pre style="margin: 0;"> <span id="LC3855" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4041" style="width: 35px; color: rgba(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="4202" style="width: 35px; color: rgba(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">@@ -4041,24 +4202,6 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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4041
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4202
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<pre style="margin: 0;"> <span id="LC4202" 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_info_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_curs</span><span class="p">[</span><span class="n" style="color: #333;">kpos</span><span class="p">];</span></span>
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4042
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4203
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<pre style="margin: 0;"> <span id="LC4203" class="line" lang="cpp"></span>
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4043
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4204
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<pre style="margin: 0;"> <span id="LC4204" 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;">subtoken_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToDelimOrEnd</span><span class="p">(</span><span class="n" style="color: #333;">cur_info_cur</span><span class="p">,</span> <span class="n" style="color: #333;">cur_info_end</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4044
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4044" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">knum</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kInfoVtypeG</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4045
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4045" 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;">subtoken_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_info_end</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4046
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4046" 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: Too few values for INFO key '%s', variant ID '%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_key_str</span><span class="p">,</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">);</span></span>
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4047
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4048
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4048" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4049
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4049" 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;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="n" style="color: #333;">cur_info_cur</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="p">,</span> <span class="n" style="color: #333;">subtoken_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cur_info_cur</span><span class="p">));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4050
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4050" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_info_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subtoken_end</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4051
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4051" 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;">skip_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt_allele_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="old_line diff-line-num old" data-linenumber="4052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4052
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">skip_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4053
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4053" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_info_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToNthDelimChecked</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">cur_info_cur</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">cur_info_end</span><span class="p">,</span> <span class="n" style="color: #333;">skip_ct</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4054
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4054" 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;">subtoken_end</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4055
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4055" 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: Too few values for INFO key '%s', variant ID '%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_key_str</span><span class="p">,</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="4056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4056
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4056" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4057
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4057" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4058
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<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4058" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="4059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4059
</td>
<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4059" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cur_info_cur</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="4060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4060
</td>
<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4060" class="line" lang="cpp"> <span class="n" style="color: #333;">subtoken_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToDelimOrEnd</span><span class="p">(</span><span class="n" style="color: #333;">cur_info_cur</span><span class="p">,</span> <span class="n" style="color: #333;">cur_info_end</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="4061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4061
</td>
<td class="new_line diff-line-num old" data-linenumber="4205" style="width: 35px; color: rgba(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="LC4061" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="4062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4062
</td>
<td class="new_line diff-line-num" data-linenumber="4205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4205
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<pre style="margin: 0;"> <span id="LC4205" 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;">subtoken_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_info_end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">is_last_allele</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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4063
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4206
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<pre style="margin: 0;"> <span id="LC4206" 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: Wrong number of values for INFO key '%s', variant ID '%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_key_str</span><span class="p">,</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">);</span></span>
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4064
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4207
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<pre style="margin: 0;"> <span id="LC4207" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4337" style="width: 35px; color: rgba(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="4480" style="width: 35px; color: rgba(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">@@ -4337,14 +4480,17 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4337
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<td class="new_line diff-line-num" data-linenumber="4480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4480
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<pre style="margin: 0;"> <span id="LC4480" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t raw_variant_ctl = BitCtToWordCt(raw_variant_ct);</span></span>
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4338
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<td class="new_line diff-line-num" data-linenumber="4481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4481
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<pre style="margin: 0;"> <span id="LC4481" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t all_nonref = (nonref_flags_storage == 2);</span></span>
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<td class="old_line diff-line-num" data-linenumber="4339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4339
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<td class="new_line diff-line-num" data-linenumber="4482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4482
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<pre style="margin: 0;"> <span id="LC4482" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t write_info_pr = all_nonref;</span></span>
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4340
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<td class="new_line diff-line-num old" data-linenumber="4483" style="width: 35px; color: rgba(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="LC4340" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t write_info = (pvar_psam_flags & kfPvarColInfo) || pvar_info_reload;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4483
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<pre style="margin: 0;">+<span id="LC4483" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_info_reload && (!(pvar_psam_flags & kfPvarColXinfo))) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4484
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<pre style="margin: 0;">+<span id="LC4484" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> pvar_info_reload = nullptr;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4485
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<pre style="margin: 0;">+<span id="LC4485" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4486
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<pre style="margin: 0;">+<span id="LC4486" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t write_info = (pvar_psam_flags & kfPvarColInfo) || pvar_info_reload;</span></span>
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4341
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4487
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<pre style="margin: 0;"> <span id="LC4487" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_info && nonref_flags) {</span></span>
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4342
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4488
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<pre style="margin: 0;"> <span id="LC4488" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_info_pr = !IntersectionIsEmpty(variant_include, nonref_flags, raw_variant_ctl);</span></span>
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4343
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<td class="new_line diff-line-num" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4489
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<pre style="margin: 0;"> <span id="LC4489" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4344
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<td class="new_line diff-line-num" data-linenumber="4490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4490
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<pre style="margin: 0;"> <span id="LC4490" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> write_info_pr = write_info_pr && write_info;</span></span>
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<td class="old_line diff-line-num" data-linenumber="4345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4345
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<td class="new_line diff-line-num" data-linenumber="4491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4491
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<pre style="margin: 0;"> <span id="LC4491" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(write_info_pr && (info_flags & kfInfoPrNonflagPresent))) {</span></span>
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4346
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<td class="new_line diff-line-num" data-linenumber="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4492
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<pre style="margin: 0;"> <span id="LC4492" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> logputs("\n");</span></span>
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4347
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<td class="new_line diff-line-num old" data-linenumber="4493" style="width: 35px; color: rgba(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="LC4347" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> logerrputs("Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the\n<span class="idiff left">'</span>provisional reference<span class="idiff right">'</span> flag is no longer needed, or remove/rename the other\nuse of the INFO/PR key.\n");</span></span>
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4493
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<pre style="margin: 0;">+<span id="LC4493" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> logerrputs("Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the\n<span class="idiff left">\"</span>provisional reference<span class="idiff right">\"</span> flag is no longer needed, or remove/rename the other\nuse of the INFO/PR key.\n");</span></span>
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4348
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<td class="new_line diff-line-num" data-linenumber="4494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4494
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<pre style="margin: 0;"> <span id="LC4494" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_INCONSISTENT_INPUT;</span></span>
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4349
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<td class="new_line diff-line-num" data-linenumber="4495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4495
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<pre style="margin: 0;"> <span id="LC4495" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4350
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4496
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<pre style="margin: 0;"> <span id="LC4496" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4736" style="width: 35px; color: rgba(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="4882" style="width: 35px; color: rgba(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">@@ -4736,7 +4882,8 @@ typedef struct MakeBedlikeCtxStruct {</td>
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4736
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4882
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<pre style="margin: 0;"> <span id="LC4882" class="line" lang="cpp"></span>
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4737
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4883
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<pre style="margin: 0;"> <span id="LC4883" 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;">variant_include</span><span class="p">;</span></span>
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4738
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4884
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<pre style="margin: 0;"> <span id="LC4884" 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;">sample_include_cumulative_popcounts</span><span class="p">;</span></span>
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4739
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<td class="new_line diff-line-num old" data-linenumber="4885" style="width: 35px; color: rgba(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="LC4739" 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;">collapsed_sort_map</span><span class="p">;</span></span>
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4885
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<pre style="margin: 0;">+<span id="LC4885" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// unlike MakePgenCtx, old_sample_idx is subsetted here</span></span>
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4886
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<pre style="margin: 0;">+<span id="LC4886" 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;">old_sample_idx_to_new</span><span class="p">;</span></span>
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4740
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4887
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<pre style="margin: 0;"> <span id="LC4887" class="line" lang="cpp"></span>
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4741
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4888
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<pre style="margin: 0;"> <span id="LC4888" class="line" lang="cpp"> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">pgr_ptrs</span><span class="p">;</span></span>
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4742
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4889
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<pre style="margin: 0;"> <span id="LC4889" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4775" style="width: 35px; color: rgba(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="4922" style="width: 35px; color: rgba(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">@@ -4775,7 +4922,7 @@ THREAD_FUNC_DECL MakeBedlikeThread(void* raw_arg) {</td>
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4775
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4922
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<pre style="margin: 0;"> <span id="LC4922" class="line" lang="cpp"> <span class="n" style="color: #333;">PgrSetSampleSubsetIndex</span><span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">pgrp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pssi</span><span class="p">);</span></span>
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4776
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4923
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<pre style="margin: 0;"> <span id="LC4923" 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;">sex_male_collapsed_interleaved</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sex_male_collapsed_interleaved</span><span class="p">;</span></span>
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4777
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4924
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<pre style="margin: 0;"> <span id="LC4924" 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;">sex_female_collapsed_interleaved</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sex_female_collapsed_interleaved</span><span class="p">;</span></span>
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4778
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<pre style="margin: 0;">-<span id="LC4778" 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;"><span class="idiff left">c</span>ol<span class="idiff">lapsed_sort_map</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff">c</span>ol<span class="idiff right">lapsed_sort_map</span></span><span class="p">;</span></span>
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4925
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<pre style="margin: 0;">+<span id="LC4925" 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;">ol<span class="idiff left">d_sample_idx_to_new</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ol<span class="idiff right">d_sample_idx_to_new</span></span><span class="p">;</span></span>
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4779
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4926
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<pre style="margin: 0;"> <span id="LC4926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Plink2WriteFlags</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;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plink2_write_flags</span><span class="p">;</span></span>
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4780
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4927
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<pre style="margin: 0;"> <span id="LC4927" 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;">set_hh_missing</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;">kfPlink2WriteSetHhMissing</span><span class="p">;</span></span>
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4781
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<td class="new_line diff-line-num" data-linenumber="4928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4928
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<pre style="margin: 0;"> <span id="LC4928" 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;">set_mixed_mt_missing</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;">kfPlink2WriteSetMixedMtMissing</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4878" style="width: 35px; color: rgba(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="5025" style="width: 35px; color: rgba(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">@@ -4878,12 +5025,11 @@ THREAD_FUNC_DECL MakeBedlikeThread(void* raw_arg) {</td>
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4878
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5025
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<pre style="margin: 0;"> <span id="LC5025" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_plink1</span><span class="p">)</span> <span class="p">{</span></span>
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4879
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<td class="new_line diff-line-num" data-linenumber="5026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5026
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<pre style="margin: 0;"> <span id="LC5026" class="line" lang="cpp"> <span class="n" style="color: #333;">PgrPlink2ToPlink1InplaceUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">genovec</span><span class="p">);</span></span>
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4880
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5027
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<pre style="margin: 0;"> <span id="LC5027" class="line" lang="cpp"> <span class="p">}</span></span>
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4881
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<pre style="margin: 0;">-<span id="LC4881" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// trailing bytes don't matter, but trailing bits of last byte may</span></span>
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4882
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5028
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<pre style="margin: 0;"> <span id="LC5028" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroTrailingNyps</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">genovec</span><span class="p">);</span></span>
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4883
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<pre style="margin: 0;">-<span id="LC4883" 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;"><span class="idiff left">c</span>ol<span class="idiff right">lapsed_sort_map</span></span><span class="p">)</span> <span class="p">{</span></span>
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5029
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<pre style="margin: 0;">+<span id="LC5029" 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;">ol<span class="idiff left right">d_sample_idx_to_new</span></span><span class="p">)</span> <span class="p">{</span></span>
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4884
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5030
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<pre style="margin: 0;"> <span id="LC5030" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyua</span><span class="p">(</span><span class="n" style="color: #333;">writebuf_iter</span><span class="p">,</span> <span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct4</span><span class="p">);</span></span>
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4885
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5031
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<pre style="margin: 0;"> <span id="LC5031" 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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4886
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<pre style="margin: 0;">-<span id="LC4886" class="line" lang="cpp"> <span class="n" style="color: #333;">Genovec<span class="idiff left">Resort</span></span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">c</span>ol<span class="idiff right">lapsed_sort_map</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">writebuf_iter</span><span class="p">);</span></span>
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5032
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<pre style="margin: 0;">+<span id="LC5032" class="line" lang="cpp"> <span class="n" style="color: #333;">Genovec<span class="idiff left">Permute</span></span><span class="p">(</span><span class="n" style="color: #333;">genovec</span><span class="p">,</span> <span class="n" style="color: #333;">ol<span class="idiff right">d_sample_idx_to_new</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">writebuf_iter</span><span class="p">);</span></span>
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4887
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5033
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<pre style="margin: 0;"> <span id="LC5033" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_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;">writebuf_iter</span><span class="p">[</span><span class="n" style="color: #333;">sample_ct4</span><span class="p">]);</span></span>
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4888
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5034
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<pre style="margin: 0;"> <span id="LC5034" class="line" lang="cpp"> <span class="p">}</span></span>
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4889
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5035
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<pre style="margin: 0;"> <span id="LC5035" 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="4957" style="width: 35px; color: rgba(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="5103" style="width: 35px; color: rgba(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">@@ -4957,7 +5103,7 @@ PglErr MakeBedlikeMain(const uintptr_t* sample_include, const uint32_t* new_samp</td>
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4957
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5103
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<pre style="margin: 0;"> <span id="LC5103" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tried more threads, pointless since this is too I/O-bound</span></span>
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4958
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5104
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<pre style="margin: 0;"> <span id="LC5104" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (exception: reordering samples)</span></span>
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4959
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5105
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<pre style="margin: 0;"> <span id="LC5105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">max_thread_ct</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;">max_thread_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;">max_thread_ct</span><span class="p">;</span></span>
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4960
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<pre style="margin: 0;">-<span id="LC4960" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">c</span>ol<span class="idiff">lapsed_sort_map</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">new_sample_idx_to_old</span></span><span class="p">;</span></span>
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5106
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<pre style="margin: 0;">+<span id="LC5106" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">ol<span class="idiff left">d_sample_idx_to_new</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 right">nullptr</span></span><span class="p">;</span></span>
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4961
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5107
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<pre style="margin: 0;"> <span id="LC5107" 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_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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4962
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5108
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<pre style="margin: 0;"> <span id="LC5108" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Without BMI2 instructions, subsetting is most expensive with</span></span>
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4963
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5109
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<pre style="margin: 0;"> <span id="LC5109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sample_ct near 2/3 of raw_sample_ct; up to ~7 compute threads are</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">@@ -4977,15 +5123,22 @@ PglErr MakeBedlikeMain(const uintptr_t* sample_include, const uint32_t* new_samp</td>
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4977
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">calc_thread_max</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="p">{</span></span>
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4978
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5124
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<pre style="margin: 0;"> <span id="LC5124" class="line" lang="cpp"> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calc_thread_max</span><span class="p">;</span></span>
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4979
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5125
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<pre style="margin: 0;"> <span id="LC5125" class="line" lang="cpp"> <span class="p">}</span></span>
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4980
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<pre style="margin: 0;">-<span id="LC4980" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sample_ct</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">raw_sample_ct</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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4981
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<pre style="margin: 0;">-<span id="LC4981" 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;"><span class="idiff left right">new_collapsed_sort_map</span></span><span class="p">;</span></span>
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4982
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<pre style="margin: 0;">-<span id="LC4982" 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;">sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left right">new_collapsed_sort_map</span></span><span class="p">)))</span> <span class="p">{</span></span>
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5126
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<pre style="margin: 0;">+<span id="LC5126" 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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5127
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<pre style="margin: 0;">+<span id="LC5127" 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;"><span class="idiff left right">old_sample_idx_to_new</span></span><span class="p">;</span></span>
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5128
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<pre style="margin: 0;">+<span id="LC5128" 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;"><span class="idiff left">raw_</span>sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff right">old_sample_idx_to_new</span></span><span class="p">)))</span> <span class="p">{</span></span>
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4983
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5129
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<pre style="margin: 0;"> <span id="LC5129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakeBedlikeMain_ret_NOMEM</span><span class="p">;</span></span>
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4984
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5130
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<pre style="margin: 0;"> <span id="LC5130" class="line" lang="cpp"> <span class="p">}</span></span>
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4985
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<pre style="margin: 0;">-<span id="LC4985" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (26 Mar 2018): forgot to initialize this</span></span>
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4986
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<pre style="margin: 0;">-<span id="LC4986" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_collapsed_sort_map</span><span class="p">,</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</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;">int32_t</span><span class="p">));</span></span>
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4987
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<pre style="margin: 0;">-<span id="LC4987" class="line" lang="cpp"> <span class="n" style="color: #333;">UidxsToIdxs</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">new_collapsed_sort_map</span><span class="p">);</span></span>
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4988
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<pre style="margin: 0;">-<span id="LC4988" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">collapsed_sort_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_collapsed_sort_map</span><span class="p">;</span></span>
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5131
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<pre style="margin: 0;">+<span id="LC5131" 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="n" style="color: #333;">raw_sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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5132
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<pre style="margin: 0;">+<span id="LC5132" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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5133
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<pre style="margin: 0;">+<span id="LC5133" class="line" lang="cpp"> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</span><span class="p">;</span></span>
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5134
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<pre style="margin: 0;">+<span id="LC5134" class="line" lang="cpp"> <span class="p">}</span></span>
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5135
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<pre style="margin: 0;">+<span id="LC5135" 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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5136
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<pre style="margin: 0;">+<span id="LC5136" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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5137
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<pre style="margin: 0;">+<span id="LC5137" 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_sample_uidx</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="n" style="color: #333;">new_sample_idx</span><span class="p">];</span></span>
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5138
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<pre style="margin: 0;">+<span id="LC5138" class="line" lang="cpp"> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">[</span><span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_uidx</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</span><span class="p">;</span></span>
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5139
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<pre style="margin: 0;">+<span id="LC5139" class="line" lang="cpp"> <span class="p">}</span></span>
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5140
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<pre style="margin: 0;">+<span id="LC5140" class="line" lang="cpp"> <span class="p">}</span></span>
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5141
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<pre style="margin: 0;">+<span id="LC5141" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">;</span></span>
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4989
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5142
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<pre style="margin: 0;"> <span id="LC5142" class="line" lang="cpp"> <span class="p">}</span></span>
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4990
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5143
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<pre style="margin: 0;"> <span id="LC5143" class="line" lang="cpp"></span>
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4991
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5144
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<pre style="margin: 0;"> <span id="LC5144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakeBed</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="5122" style="width: 35px; color: rgba(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="5275" style="width: 35px; color: rgba(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">@@ -5122,8 +5275,8 @@ PglErr MakeBedlikeMain(const uintptr_t* sample_include, const uint32_t* new_samp</td>
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5122
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5275
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<pre style="margin: 0;"> <span id="LC5275" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">MakePgenCtxStruct</span> <span class="p">{</span></span>
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5123
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5276
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<pre style="margin: 0;"> <span id="LC5276" class="line" lang="cpp"> <span class="n" style="color: #333;">MakeCommon</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mcp</span><span class="p">;</span></span>
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5124
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5277
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<pre style="margin: 0;"> <span id="LC5277" class="line" lang="cpp"></span>
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5125
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<pre style="margin: 0;">-<span id="LC5125" 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;">new_sample_idx_to_old</span><span class="p">;</span></span>
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5126
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5278
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<pre style="margin: 0;"> <span id="LC5278" 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;">old_sample_idx_to_new</span><span class="p">;</span></span>
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5279
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<pre style="margin: 0;">+<span id="LC5279" 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;">sample_include_interleaved_vec</span><span class="p">;</span></span>
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5127
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5280
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<pre style="margin: 0;"> <span id="LC5280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// combine existing chr_mask/xymt_codes/haploid_mask/chr_idx_to_foidx with</span></span>
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5128
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5281
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<pre style="margin: 0;"> <span id="LC5281" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// new collapsed chromosome boundary table</span></span>
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5129
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5282
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<pre style="margin: 0;"> <span id="LC5282" 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;">write_chr_fo_vidx_start</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5150" style="width: 35px; color: rgba(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="5303" style="width: 35px; color: rgba(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">@@ -5150,7 +5303,6 @@ typedef struct MakePgenCtxStruct {</td>
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5150
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5303
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<pre style="margin: 0;"> <span id="LC5303" class="line" lang="cpp"> <span class="n" style="color: #333;">Dosage</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">thread_write_dosagevals</span><span class="p">;</span></span>
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5151
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5304
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<pre style="margin: 0;"> <span id="LC5304" 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;">thread_write_dphasepresents</span><span class="p">;</span></span>
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5152
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<td class="new_line diff-line-num" data-linenumber="5305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5305
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<pre style="margin: 0;"> <span id="LC5305" class="line" lang="cpp"> <span class="n" style="color: #333;">SDosage</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">thread_write_dphasedeltas</span><span class="p">;</span></span>
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5153
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<td class="new_line diff-line-num old" data-linenumber="5306" style="width: 35px; color: rgba(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="LC5153" 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;">thread_cumulative_popcount_bufs</span><span class="p">;</span></span>
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5154
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5306
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<pre style="margin: 0;"> <span id="LC5306" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">write_reterr</span><span class="p">;</span></span>
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5155
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5307
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<pre style="margin: 0;"> <span id="LC5307" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">write_errno</span><span class="p">;</span></span>
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5156
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5308
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<pre style="margin: 0;"> <span id="LC5308" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">MakePgenCtx</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5168" style="width: 35px; color: rgba(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="5320" style="width: 35px; color: rgba(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">@@ -5168,7 +5320,6 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5168
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5320
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<pre style="margin: 0;"> <span id="LC5320" 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;">tidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tidx</span><span class="p">;</span></span>
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5169
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5321
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<pre style="margin: 0;"> <span id="LC5321" class="line" lang="cpp"> <span class="n" style="color: #333;">MakePgenCtx</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ctx</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;">MakePgenCtx</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sharedp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">context</span><span class="p">);</span></span>
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5170
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5322
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<pre style="margin: 0;"> <span id="LC5322" class="line" lang="cpp"></span>
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5171
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<pre style="margin: 0;">-<span id="LC5171" 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;">new_sample_idx_to_old</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</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>
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5172
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5323
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<pre style="margin: 0;"> <span id="LC5323" 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;">old_sample_idx_to_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">old_sample_idx_to_new</span><span class="p">;</span></span>
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5173
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5324
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<pre style="margin: 0;"> <span id="LC5324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MakeCommon</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mcp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mcp</span><span class="p">;</span></span>
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5174
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5325
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<pre style="margin: 0;"> <span id="LC5325" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mcp</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 old_line" data-linenumber="5176" style="width: 35px; color: rgba(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="5327" style="width: 35px; color: rgba(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">@@ -5176,6 +5327,7 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5176
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5327
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<pre style="margin: 0;"> <span id="LC5327" 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;">write_allele_idx_offsets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">write_allele_idx_offsets</span><span class="p">;</span></span>
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5177
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5328
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<pre style="margin: 0;"> <span id="LC5328" class="line" lang="cpp"> <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_iter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refalt1_select</span><span class="p">;</span></span>
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5178
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5329
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<pre style="margin: 0;"> <span id="LC5329" 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;">sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mcp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_include</span><span class="p">;</span></span>
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5330
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<pre style="margin: 0;">+<span id="LC5330" 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;">sample_include_interleaved_vec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_include_interleaved_vec</span><span class="p">;</span></span>
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5179
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5331
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<pre style="margin: 0;"> <span id="LC5331" class="line" lang="cpp"></span>
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5180
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5332
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<pre style="margin: 0;"> <span id="LC5332" 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;">sex_male_collapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sex_male_collapsed</span><span class="p">;</span></span>
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5181
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5333
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<pre style="margin: 0;"> <span id="LC5333" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5216" style="width: 35px; color: rgba(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="5368" style="width: 35px; color: rgba(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">@@ -5216,7 +5368,7 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5216
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5368
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<pre style="margin: 0;"> <span id="LC5368" class="line" lang="cpp"> <span class="p">}</span></span>
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5217
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5369
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<pre style="margin: 0;"> <span id="LC5369" 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;">write_genovec</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="old_line diff-line-num" data-linenumber="5218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5218
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<td class="new_line diff-line-num" data-linenumber="5370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5370
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<pre style="margin: 0;"> <span id="LC5370" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assumes sample_include == nullptr if sample_ct == raw_sample_ct</span></span>
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5219
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<td class="new_line diff-line-num old" data-linenumber="5371" style="width: 35px; color: rgba(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="LC5219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">new</span>_sample_idx_to_<span class="idiff right">old</span></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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5371
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<pre style="margin: 0;">+<span id="LC5371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">old</span>_sample_idx_to_<span class="idiff right">new</span></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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5220
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5372
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<pre style="margin: 0;"> <span id="LC5372" class="line" lang="cpp"> <span class="n" style="color: #333;">write_genovec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_genovecs</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">];</span></span>
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5221
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5373
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<pre style="margin: 0;"> <span id="LC5373" class="line" lang="cpp"> <span class="n" style="color: #333;">write_genovec</span><span class="p">[</span><span class="n" style="color: #333;">sample_ctl2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5222
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5374
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<pre style="margin: 0;"> <span id="LC5374" 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="5242" style="width: 35px; color: rgba(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="5394" style="width: 35px; color: rgba(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">@@ -5242,7 +5394,6 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5242
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5394
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<pre style="margin: 0;"> <span id="LC5394" 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;">write_dphasepresent</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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5243
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5395
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<pre style="margin: 0;"> <span id="LC5395" class="line" lang="cpp"> <span class="n" style="color: #333;">SDosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_dphasedeltas</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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5244
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5396
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<pre style="margin: 0;"> <span id="LC5396" class="line" lang="cpp"> <span class="n" style="color: #333;">SDosage</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp_dphasedeltas</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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5245
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<pre style="margin: 0;">-<span id="LC5245" 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;">cumulative_popcount_buf</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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5246
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5397
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<pre style="margin: 0;"> <span id="LC5397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_dosagepresents</span><span class="p">)</span> <span class="p">{</span></span>
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5247
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5398
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<pre style="margin: 0;"> <span id="LC5398" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dosagepresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_dosagepresents</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">];</span></span>
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5248
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5399
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<pre style="margin: 0;"> <span id="LC5399" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dosagevals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_dosagevals</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5252" style="width: 35px; color: rgba(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="5403" style="width: 35px; color: rgba(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">@@ -5252,9 +5403,6 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5252
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5403
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<pre style="margin: 0;"> <span id="LC5403" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_dphasedeltas</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;">write_dphasedeltas</span><span class="p">[</span><span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</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>
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5253
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5404
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<pre style="margin: 0;"> <span id="LC5404" class="line" lang="cpp"> <span class="p">}</span></span>
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5254
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5405
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<pre style="margin: 0;"> <span id="LC5405" class="line" lang="cpp"> <span class="p">}</span></span>
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5255
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<pre style="margin: 0;">-<span id="LC5255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_mhc</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_write_dosagepresents</span><span class="p">)</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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5256
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<pre style="margin: 0;">-<span id="LC5256" class="line" lang="cpp"> <span class="n" style="color: #333;">cumulative_popcount_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ctx</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">thread_cumulative_popcount_bufs</span><span class="p">[</span><span class="n" style="color: #333;">tidx</span><span class="p">];</span></span>
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5257
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<pre style="margin: 0;">-<span id="LC5257" class="line" lang="cpp"> <span class="p">}</span></span>
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5258
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5406
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<pre style="margin: 0;"> <span id="LC5406" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_idx_offset</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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5259
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5407
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<pre style="margin: 0;"> <span id="LC5407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</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>
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5260
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5408
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<pre style="margin: 0;"> <span id="LC5408" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5369" style="width: 35px; color: rgba(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="5517" style="width: 35px; color: rgba(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">@@ -5369,21 +5517,22 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {</td>
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5369
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5517
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<pre style="margin: 0;"> <span id="LC5517" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_rare10_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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5370
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5518
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<pre style="margin: 0;"> <span id="LC5518" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_dosage_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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5371
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5519
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<pre style="margin: 0;"> <span id="LC5519" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_dphase_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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5372
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<pre style="margin: 0;">-<span id="LC5372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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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5373
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<td class="new_line diff-line-num old" data-linenumber="5520" style="width: 35px; color: rgba(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="LC5373" class="line" lang="cpp"> <span class="n" style="color: #333;">GenovecResort</span><span class="p">(</span><span class="n" style="color: #333;">loadbuf_iter</span><span class="p">,</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_genovec</span><span class="p">);</span></span>
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5520
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<pre style="margin: 0;">+<span id="LC5520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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>
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<td class="new_line diff-line-num new" data-linenumber="5521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5521
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<pre style="margin: 0;">+<span id="LC5521" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroTrailingNyps</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;">loadbuf_iter</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5522
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<pre style="margin: 0;">+<span id="LC5522" class="line" lang="cpp"> <span class="n" style="color: #333;">GenovecPermuteSubset</span><span class="p">(</span><span class="n" style="color: #333;">loadbuf_iter</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_include_interleaved_vec</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">write_genovec</span><span class="p">);</span></span>
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5374
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<td class="new_line diff-line-num" data-linenumber="5523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5523
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<pre style="margin: 0;"> <span id="LC5523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_rare01_ct</span><span class="p">)</span> <span class="p">{</span></span>
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5375
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<td class="new_line diff-line-num old" data-linenumber="5524" style="width: 35px; color: rgba(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="LC5375" class="line" lang="cpp"> <span class="n" style="color: #333;">write_rare01_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Resort8bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">read_patch_01_set</span><span class="p">,</span> <span class="n" style="color: #333;">read_patch_01_vals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">new</span>_sample_idx_to_<span class="idiff">old</span></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;"><span class="idiff">sample</span>_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_01_set</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_01_vals</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cumulative_popcount_buf</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5376" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="5524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5524
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<pre style="margin: 0;">+<span id="LC5524" class="line" lang="cpp"> <span class="n" style="color: #333;">write_rare01_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Permute8bit</span></span><span class="p"><span class="idiff">(</span></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="n" style="color: #333;">read_patch_01_set</span><span class="p">,</span> <span class="n" style="color: #333;">read_patch_01_vals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">old</span>_sample_idx_to_<span class="idiff">new</span></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;"><span class="idiff right">read_rare01</span>_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_01_set</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_01_vals</span><span class="p">);</span></span>
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5376
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<td class="new_line diff-line-num" data-linenumber="5525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5525
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<pre style="margin: 0;"> <span id="LC5525" class="line" lang="cpp"> <span class="p">}</span></span>
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5377
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<td class="new_line diff-line-num" data-linenumber="5526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5526
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<pre style="margin: 0;"> <span id="LC5526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read_rare10_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5378
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<td class="new_line diff-line-num old" data-linenumber="5527" style="width: 35px; color: rgba(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="LC5378" class="line" lang="cpp"> <span class="n" style="color: #333;">write_rare10_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Resort16bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">read_patch_10_set</span><span class="p">,</span> <span class="n" style="color: #333;">read_patch_10_vals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">new</span>_sample_idx_to_<span class="idiff">old</span></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;"><span class="idiff">sample</span>_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_10_set</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_10_vals</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cumulative_popcount_buf</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5379" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="5527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5527
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<pre style="margin: 0;">+<span id="LC5527" class="line" lang="cpp"> <span class="n" style="color: #333;">write_rare10_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Permute16bit</span></span><span class="p"><span class="idiff">(</span></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="n" style="color: #333;">read_patch_10_set</span><span class="p">,</span> <span class="n" style="color: #333;">read_patch_10_vals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">old</span>_sample_idx_to_<span class="idiff">new</span></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;"><span class="idiff right">read_rare10</span>_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_10_set</span><span class="p">,</span> <span class="n" style="color: #333;">write_patch_10_vals</span><span class="p">);</span></span>
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5379
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<td class="new_line diff-line-num" data-linenumber="5528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5528
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<pre style="margin: 0;"> <span id="LC5528" class="line" lang="cpp"> <span class="p">}</span></span>
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5380
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<td class="new_line diff-line-num" data-linenumber="5529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5529
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<pre style="margin: 0;"> <span id="LC5529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_hphase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5381
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<td class="new_line diff-line-num old" data-linenumber="5530" style="width: 35px; color: rgba(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="LC5381" class="line" lang="cpp"> <span class="n" style="color: #333;">UnpackAnd<span class="idiff left right">Resort</span>Hphase</span><span class="p">(</span><span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">cur_phaseraw</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_write_phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_phaseinfo</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5382" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="5530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5530
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<pre style="margin: 0;">+<span id="LC5530" class="line" lang="cpp"> <span class="n" style="color: #333;">UnpackAnd<span class="idiff left right">Permute</span>Hphase</span><span class="p">(</span><span class="n" style="color: #333;">all_hets</span><span class="p">,</span> <span class="n" style="color: #333;">cur_phaseraw</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_write_phasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_phaseinfo</span><span class="p">);</span></span>
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5382
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<td class="new_line diff-line-num" data-linenumber="5531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5531
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<pre style="margin: 0;"> <span id="LC5531" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="5383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5383
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<td class="new_line diff-line-num" data-linenumber="5532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5532
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<pre style="margin: 0;"> <span id="LC5532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dosage</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5384
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<td class="new_line diff-line-num old" data-linenumber="5533" style="width: 35px; color: rgba(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="LC5384" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dosage_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Resort16bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">cur_dosagepresent</span><span class="p">,</span> <span class="n" style="color: #333;">cur_dosagevals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">new</span>_sample_idx_to_<span class="idiff">old</span></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;"><span class="idiff">sampl</span>e_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_dosagepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_dosagevals</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cumulative_popcount_buf</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="5385" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="5533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5533
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<pre style="margin: 0;">+<span id="LC5533" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dosage_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Permute16bit</span></span><span class="p"><span class="idiff">(</span></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="n" style="color: #333;">cur_dosagepresent</span><span class="p">,</span> <span class="n" style="color: #333;">cur_dosagevals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">old</span>_sample_idx_to_<span class="idiff">new</span></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;"><span class="idiff right">read_dosag</span>e_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_dosagepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_dosagevals</span><span class="p">);</span></span>
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5385
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<td class="new_line diff-line-num" data-linenumber="5534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5534
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<pre style="margin: 0;"> <span id="LC5534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dphase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5386
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<td class="new_line diff-line-num old" data-linenumber="5535" style="width: 35px; color: rgba(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="LC5386" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dphase_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Resort16bit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">cur_dphasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">cur_dphasedelta</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">new</span>_sample_idx_to_<span class="idiff">old</span></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;"><span class="idiff">sampl</span>e_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_dphasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_dphasedeltas</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cumulative_popcount_buf</span></span><span class="p">);</span></span>
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5535
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<pre style="margin: 0;">+<span id="LC5535" class="line" lang="cpp"> <span class="n" style="color: #333;">write_dphase_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CopyAnd<span class="idiff left">Permute16bit</span></span><span class="p"><span class="idiff">(</span></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="n" style="color: #333;">cur_dphasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">cur_dphasedelta</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">old</span>_sample_idx_to_<span class="idiff">new</span></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;"><span class="idiff right">read_dphas</span>e_ct</span><span class="p">,</span> <span class="n" style="color: #333;">write_dphasepresent</span><span class="p">,</span> <span class="n" style="color: #333;">write_dphasedeltas</span><span class="p">);</span></span>
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5387
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5536
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<pre style="margin: 0;"> <span id="LC5536" class="line" lang="cpp"> <span class="p">}</span></span>
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5388
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5537
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<pre style="margin: 0;"> <span id="LC5537" class="line" lang="cpp"> <span class="p">}</span></span>
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5389
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5538
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<pre style="margin: 0;"> <span id="LC5538" 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;">sample_include</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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6014" style="width: 35px; color: rgba(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">@@ -5865,7 +6014,6 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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5865
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6014
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<pre style="margin: 0;"> <span id="LC6014" 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;">subsetting_required</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="n" style="color: #333;">raw_sample_ct</span><span class="p">);</span></span>
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5866
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6015
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<pre style="margin: 0;"> <span id="LC6015" 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_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;">raw_sample_ct</span><span class="p">);</span></span>
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5867
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<td class="new_line diff-line-num" data-linenumber="6016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6016
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<pre style="margin: 0;"> <span id="LC6016" 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;">sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subsetting_required</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">sample_include</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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5868
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<td class="new_line diff-line-num old" data-linenumber="6017" style="width: 35px; color: rgba(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="LC5868" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">new_sample_idx_to_old</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>
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5869
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6017
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<pre style="margin: 0;"> <span id="LC6017" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sex_male_collapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sex_male_collapsed</span><span class="p">;</span></span>
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5870
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6018
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<pre style="margin: 0;"> <span id="LC6018" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sex_female_collapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sex_female_collapsed</span><span class="p">;</span></span>
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5871
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6019
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<pre style="margin: 0;"> <span id="LC6019" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">write_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="6017" style="width: 35px; color: rgba(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="6165" style="width: 35px; color: rgba(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">@@ -6017,15 +6165,25 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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6017
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6165
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<pre style="margin: 0;"> <span id="LC6165" 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;">NypCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">);</span></span>
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6018
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6166
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<pre style="margin: 0;"> <span id="LC6166" 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_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;">sample_ct</span><span class="p">);</span></span>
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6019
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6167
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<pre style="margin: 0;"> <span id="LC6167" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_genovecs</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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6168
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<pre style="margin: 0;">+<span id="LC6168" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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6169
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<pre style="margin: 0;">+<span id="LC6169" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</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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6020
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6170
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<pre style="margin: 0;"> <span id="LC6170" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_mhc_needed</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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6021
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6171
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<pre style="margin: 0;"> <span id="LC6171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">new_sample_idx_to_old</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">subsetting_required</span><span class="p">)</span> <span class="p">{</span></span>
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6022
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6172
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<pre style="margin: 0;"> <span id="LC6172" 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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6023
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<td class="new_line diff-line-num" data-linenumber="6173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6173" 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="old_line diff-line-num" data-linenumber="6024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6024
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<td class="new_line diff-line-num" data-linenumber="6174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6174
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<pre style="margin: 0;"> <span id="LC6174" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="6025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6025
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<td class="new_line diff-line-num old" data-linenumber="6175" style="width: 35px; color: rgba(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="LC6025" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">read_phase_present</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="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="old_line diff-line-num new" data-linenumber="6026" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6175
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<pre style="margin: 0;">+<span id="LC6175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="old_line diff-line-num" data-linenumber="6026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6026
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<td class="new_line diff-line-num" data-linenumber="6176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6176
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<pre style="margin: 0;"> <span id="LC6176" 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="old_line diff-line-num" data-linenumber="6027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6027
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<td class="new_line diff-line-num" data-linenumber="6177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6177
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<pre style="margin: 0;"> <span id="LC6177" 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="old_line diff-line-num" data-linenumber="6028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6028
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<td class="new_line diff-line-num" data-linenumber="6178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6178
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<pre style="margin: 0;"> <span id="LC6178" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6179
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<pre style="margin: 0;">+<span id="LC6179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subsetting_required</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6180
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<pre style="margin: 0;">+<span id="LC6180" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SetAllU32Arr(raw_sample_ct, ctx.old_sample_idx_to_new);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6181
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<pre style="margin: 0;">+<span id="LC6181" 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_ctv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6182
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<pre style="margin: 0;">+<span id="LC6182" 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_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctv</span> <span class="o" style="font-weight: 600;">*</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6183
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<pre style="margin: 0;">+<span id="LC6183" 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="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6184
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<pre style="margin: 0;">+<span id="LC6184" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="6029" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="6185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6185
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<pre style="margin: 0;">+<span id="LC6185" class="line" lang="cpp"> <span class="n" style="color: #333;">FillInterleavedMaskVec</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctv</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</span><span class="p">);</span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="6186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6186
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<pre style="margin: 0;">+<span id="LC6186" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6029
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<td class="new_line diff-line-num" data-linenumber="6187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6187
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6187" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6030
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<td class="new_line diff-line-num" data-linenumber="6188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6188
</td>
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<pre style="margin: 0;"> <span id="LC6188" class="line" lang="cpp"> <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="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6031
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<td class="new_line diff-line-num" data-linenumber="6189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6189
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<pre style="margin: 0;"> <span id="LC6189" 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="6080" style="width: 35px; color: rgba(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="6238" style="width: 35px; color: rgba(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">@@ -6080,12 +6238,6 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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6080
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6238
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<pre style="margin: 0;"> <span id="LC6238" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6081
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6239
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<pre style="margin: 0;"> <span id="LC6239" class="line" lang="cpp"> <span class="p">}</span></span>
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6082
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6240
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<pre style="margin: 0;"> <span id="LC6240" class="line" lang="cpp"> <span class="p">}</span></span>
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6083
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<pre style="margin: 0;">-<span id="LC6083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">write_mhc_needed</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="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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6084
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<td class="new_line diff-line-num old" data-linenumber="6241" style="width: 35px; color: rgba(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="LC6084" 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_u32p</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_cumulative_popcount_bufs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6085
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<pre style="margin: 0;">-<span id="LC6085" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32</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_cumulative_popcount_bufs</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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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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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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6088
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<pre style="margin: 0;">-<span id="LC6088" class="line" lang="cpp"> <span class="p">}</span></span>
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6089
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6241
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<pre style="margin: 0;"> <span id="LC6241" 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;">refalt1_select</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">;</span></span>
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6090
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6242
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<pre style="margin: 0;"> <span id="LC6242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">refalt1_select</span><span class="p">)</span> <span class="p">{</span></span>
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6091
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6243
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<pre style="margin: 0;"> <span id="LC6243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_allele_idx_offsets</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="6159" style="width: 35px; color: rgba(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="6311" style="width: 35px; color: rgba(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">@@ -6159,7 +6311,27 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl</td>
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6159
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6311
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<pre style="margin: 0;"> <span id="LC6311" class="line" lang="cpp"></span>
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6160
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6312
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<pre style="margin: 0;"> <span id="LC6312" 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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6161
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6313
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<pre style="margin: 0;"> <span id="LC6313" 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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6162
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<pre style="margin: 0;">-<span id="LC6162" 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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6314
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<pre style="margin: 0;">+<span id="LC6314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (8 Jun 2021): forgot to include multiallelic track in</span></span>
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6315
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<pre style="margin: 0;">+<span id="LC6315" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// load_variant_vec_ct computation</span></span>
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6316
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<pre style="margin: 0;">+<span id="LC6316" 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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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6317
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<pre style="margin: 0;">+<span id="LC6317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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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6318
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<pre style="margin: 0;">+<span id="LC6318" 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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6319
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<pre style="margin: 0;">+<span id="LC6319" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// raw format:</span></span>
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6320
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<pre style="margin: 0;">+<span id="LC6320" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// rare01_ct, padded out to a word</span></span>
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6321
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<pre style="margin: 0;">+<span id="LC6321" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// rare10_ct, padded out to a word</span></span>
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6322
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<pre style="margin: 0;">+<span id="LC6322" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [round up to vector boundary, for patch_01_set]</span></span>
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6323
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<pre style="margin: 0;">+<span id="LC6323" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// aux1a, if not mode 15:</span></span>
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6324
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<pre style="margin: 0;">+<span id="LC6324" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// patch_01_set as bitarray, raw_sample_ctl words</span></span>
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6325
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<pre style="margin: 0;">+<span id="LC6325" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// patch_01_vals (raw_sample_ct * sizeof(AlleleCode)), round up to</span></span>
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6326
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<pre style="margin: 0;">+<span id="LC6326" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// word boundary</span></span>
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6327
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<pre style="margin: 0;">+<span id="LC6327" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [round up to vector boundary, for patch_10_set]</span></span>
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6328
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<pre style="margin: 0;">+<span id="LC6328" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// aux1b, if not mode 15:</span></span>
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6329
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<pre style="margin: 0;">+<span id="LC6329" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// patch_10_set as bitarray, raw_sample_ctl words</span></span>
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6330
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<pre style="margin: 0;">+<span id="LC6330" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// patch_10_vals (raw_sample_ct * 2 * sizeof(AlleleCode)), round up</span></span>
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6331
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<pre style="margin: 0;">+<span id="LC6331" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// to word boundary</span></span>
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6332
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<pre style="margin: 0;">+<span id="LC6332" 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;">multiallelic_raw_vec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WordCtToVecCt</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;">WordCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</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;">raw_sample_ct</span> <span class="o" style="font-weight: 600;">*</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="n" style="color: #333;">kBytesPerWord</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">WordCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</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;">raw_sample_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="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="n" style="color: #333;">kBytesPerWord</span><span class="p">));</span></span>
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6333
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<pre style="margin: 0;">+<span id="LC6333" class="line" lang="cpp"> <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;">WordCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">multiallelic_raw_vec_ct</span><span class="p">);</span></span>
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6334
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<pre style="margin: 0;">+<span id="LC6334" class="line" lang="cpp"> <span class="p">}</span></span>
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6163
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6335
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<pre style="margin: 0;"> <span id="LC6335" 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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6164
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6336
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<pre style="margin: 0;"> <span id="LC6336" 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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6165
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6337
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<pre style="margin: 0;"> <span id="LC6337" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6837,7 +7009,6 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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6837
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7009
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<pre style="margin: 0;"> <span id="LC7009" class="line" lang="cpp"> <span class="p">}</span></span>
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6838
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7010
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<pre style="margin: 0;"> <span id="LC7010" class="line" lang="cpp"> <span class="n" style="color: #333;">MakeCommon</span> <span class="n" style="color: #333;">mc</span><span class="p">;</span></span>
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6839
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7011
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<pre style="margin: 0;"> <span id="LC7011" class="line" lang="cpp"> <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;">kfPlink2Write0</span><span class="p">;</span></span>
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6840
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<td class="new_line diff-line-num old" data-linenumber="7012" style="width: 35px; color: rgba(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="LC6840" 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_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;">raw_sample_ct</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" 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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7012
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<pre style="margin: 0;"> <span id="LC7012" 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_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;">sample_ct</span><span class="p">);</span></span>
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6842
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7013
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<pre style="margin: 0;"> <span id="LC7013" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sex_male_collapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// defensive</span></span>
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6843
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7014
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<pre style="margin: 0;"> <span id="LC7014" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2SetHhMissing</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="7024" style="width: 35px; color: rgba(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="7195" style="width: 35px; color: rgba(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">@@ -7024,9 +7195,9 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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7024
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<td class="new_line diff-line-num" data-linenumber="7195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7195
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<pre style="margin: 0;"> <span id="LC7195" 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_sample_idx_to_old</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7025
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<td class="new_line diff-line-num" data-linenumber="7196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7196
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<pre style="margin: 0;"> <span id="LC7196" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// hphase doesn't seem to affect read:write ratio much</span></span>
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<td class="old_line diff-line-num" data-linenumber="7026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7026
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<td class="new_line diff-line-num" data-linenumber="7197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7197
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<pre style="margin: 0;"> <span id="LC7197" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_AVX2</span></span>
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7027
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<td class="new_line diff-line-num old" data-linenumber="7198" style="width: 35px; color: rgba(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="LC7027" 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;">max_calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="7028" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7198
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<pre style="margin: 0;">+<span id="LC7198" 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;">max_calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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7028
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<td class="new_line diff-line-num" data-linenumber="7199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7199
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<pre style="margin: 0;"> <span id="LC7199" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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7029
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<td class="new_line diff-line-num old" data-linenumber="7200" style="width: 35px; color: rgba(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="LC7029" 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;">max_calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subsetting_required</span><span class="p">;</span></span>
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7200
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<pre style="margin: 0;">+<span id="LC7200" 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;">max_calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subsetting_required</span><span class="p">;</span></span>
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7030
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<td class="new_line diff-line-num" data-linenumber="7201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7201
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<pre style="margin: 0;"> <span id="LC7201" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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7031
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<td class="new_line diff-line-num" data-linenumber="7202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7202
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<pre style="margin: 0;"> <span id="LC7202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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;">max_calc_thread_ct</span><span class="p">)</span> <span class="p">{</span></span>
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7032
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<td class="new_line diff-line-num" data-linenumber="7203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7203
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<pre style="margin: 0;"> <span id="LC7203" class="line" lang="cpp"> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_calc_thread_ct</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7099" style="width: 35px; color: rgba(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="7270" style="width: 35px; color: rgba(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">@@ -7099,7 +7270,6 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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7099
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<td class="new_line diff-line-num" data-linenumber="7270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7270
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<pre style="margin: 0;"> <span id="LC7270" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="7100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7100
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<td class="new_line diff-line-num" data-linenumber="7271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7271
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<pre style="margin: 0;"> <span id="LC7271" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="7101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7101
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<td class="new_line diff-line-num" data-linenumber="7272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7272
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<pre style="margin: 0;"> <span id="LC7272" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">pwcs</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;">mpgwp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pwcs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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7102
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<td class="new_line diff-line-num old" data-linenumber="7273" style="width: 35px; color: rgba(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="LC7102" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">new_sample_idx_to_old</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>
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7103
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<td class="new_line diff-line-num" data-linenumber="7273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7273
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<pre style="margin: 0;"> <span id="LC7273" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_genovecs</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="old_line diff-line-num" data-linenumber="7104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7104
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<td class="new_line diff-line-num" data-linenumber="7274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7274
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<pre style="margin: 0;"> <span id="LC7274" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_mhc</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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7105
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<td class="new_line diff-line-num" data-linenumber="7275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7275
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<pre style="margin: 0;"> <span id="LC7275" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7107" style="width: 35px; color: rgba(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="7277" style="width: 35px; color: rgba(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">@@ -7107,15 +7277,26 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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7107
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<td class="new_line diff-line-num" data-linenumber="7277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7277
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<pre style="margin: 0;"> <span id="LC7277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the I/O thread loads the next (64k * thread_ct).</span></span>
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<td class="old_line diff-line-num" data-linenumber="7108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7108
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<td class="new_line diff-line-num" data-linenumber="7278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7278
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<pre style="margin: 0;"> <span id="LC7278" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <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="n" style="color: #333;">load_vblock_cacheline_ct</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="7109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7109
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<td class="new_line diff-line-num" data-linenumber="7279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7279
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<pre style="margin: 0;"> <span id="LC7279" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num new" data-linenumber="7110" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7280
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<pre style="margin: 0;">+<span id="LC7280" class="line" lang="cpp"> <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="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="new_line diff-line-num new" data-linenumber="7281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7281
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<pre style="margin: 0;">+<span id="LC7281" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</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="old_line diff-line-num new" data-linenumber="7110" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7282
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<pre style="margin: 0;">+<span id="LC7282" class="line" lang="cpp"></span>
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7110
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<td class="new_line diff-line-num" data-linenumber="7283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7283
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<pre style="margin: 0;"> <span id="LC7283" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_mhc_needed</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="old_line diff-line-num" data-linenumber="7111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7111
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<td class="new_line diff-line-num" data-linenumber="7284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7284
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<pre style="margin: 0;"> <span id="LC7284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">new_sample_idx_to_old</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">subsetting_required</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7112
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<td class="new_line diff-line-num" data-linenumber="7285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7285
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<pre style="margin: 0;"> <span id="LC7285" 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>
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<td class="old_line diff-line-num" data-linenumber="7113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7113
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<td class="new_line diff-line-num" data-linenumber="7286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7286
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<pre style="margin: 0;"> <span id="LC7286" 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="old_line diff-line-num" data-linenumber="7114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7114
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<td class="new_line diff-line-num" data-linenumber="7287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7287
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<pre style="margin: 0;"> <span id="LC7287" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7115
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<td class="new_line diff-line-num old" data-linenumber="7288" style="width: 35px; color: rgba(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="LC7115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">read_phase_present</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="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="old_line diff-line-num old" data-linenumber="7116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7116
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<td class="new_line diff-line-num old" data-linenumber="7288" style="width: 35px; color: rgba(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="LC7116" 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>
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<td class="old_line diff-line-num new" data-linenumber="7117" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7288
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<pre style="margin: 0;">+<span id="LC7288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="old_line diff-line-num new" data-linenumber="7117" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7289
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<pre style="margin: 0;">+<span id="LC7289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">unlikely</span></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 class="idiff right">)</span></span> <span class="p">{</span></span>
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7117
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<td class="new_line diff-line-num" data-linenumber="7290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7290
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7290" 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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7118
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<td class="new_line diff-line-num" data-linenumber="7291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7291
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<pre style="margin: 0;"> <span id="LC7291" class="line" lang="cpp"> <span class="p">}</span></span>
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7292
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<pre style="margin: 0;">+<span id="LC7292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subsetting_required</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7293
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<pre style="margin: 0;">+<span id="LC7293" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SetAllU32Arr(raw_sample_ct, ctx.old_sample_idx_to_new);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7294
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<pre style="margin: 0;">+<span id="LC7294" 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_ctv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToVecCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ct</span><span class="p">);</span></span>
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7295
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<pre style="margin: 0;">+<span id="LC7295" 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_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctv</span> <span class="o" style="font-weight: 600;">*</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7296
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<pre style="margin: 0;">+<span id="LC7296" 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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7297
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<pre style="margin: 0;">+<span id="LC7297" class="line" lang="cpp"> <span class="p">}</span></span>
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7298
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<pre style="margin: 0;">+<span id="LC7298" class="line" lang="cpp"> <span class="n" style="color: #333;">FillInterleavedMaskVec</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctv</span><span class="p">,</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sample_include_interleaved_vec</span><span class="p">);</span></span>
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7299
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<pre style="margin: 0;">+<span id="LC7299" class="line" lang="cpp"> <span class="p">}</span></span>
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7119
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7300
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<pre style="margin: 0;"> <span id="LC7300" 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_sample_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;">new_sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">new_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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7120
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7301
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<pre style="margin: 0;"> <span id="LC7301" class="line" lang="cpp"> <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="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">new_sample_idx</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx</span><span class="p">;</span></span>
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7121
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7302
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<pre style="margin: 0;"> <span id="LC7302" 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="7134" style="width: 35px; color: rgba(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="7315" style="width: 35px; color: rgba(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">@@ -7134,13 +7315,6 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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7134
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7315
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<pre style="margin: 0;"> <span id="LC7315" class="line" lang="cpp"> <span class="n" style="color: #333;">write_mhcraw_cacheline_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;">mhcwrite_word_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kWordsPerCacheline</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="7135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7135
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<td class="new_line diff-line-num" data-linenumber="7316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7316
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<pre style="margin: 0;"> <span id="LC7316" 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="n" style="color: #333;">write_mhcraw_cacheline_ct</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" 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">
7136
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<td class="new_line diff-line-num" data-linenumber="7317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7317
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<pre style="margin: 0;"> <span id="LC7317" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7137
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<td class="new_line diff-line-num old" data-linenumber="7318" style="width: 35px; color: rgba(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="LC7137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">write_mhc_needed</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="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="old_line diff-line-num old" data-linenumber="7138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7138
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<td class="new_line diff-line-num old" data-linenumber="7318" style="width: 35px; color: rgba(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="LC7138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ctx.thread_cumulative_popcount_bufs</span></span>
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<td class="old_line diff-line-num 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">
7139
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<td class="new_line diff-line-num old" data-linenumber="7318" style="width: 35px; color: rgba(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="LC7139" 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="n" style="color: #333;">Int32CtToCachelineCt</span><span class="p">(</span><span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7140
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<td class="new_line diff-line-num old" data-linenumber="7318" style="width: 35px; color: rgba(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="LC7140" 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_u32p</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_cumulative_popcount_bufs</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7141
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<td class="new_line diff-line-num old" data-linenumber="7318" style="width: 35px; color: rgba(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="LC7141" 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="old_line diff-line-num old" data-linenumber="7142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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7143
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<pre style="margin: 0;">-<span id="LC7143" class="line" lang="cpp"> <span class="p">}</span></span>
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7144
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7318
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<pre style="margin: 0;"> <span id="LC7318" 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>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="7319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7319
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<pre style="margin: 0;"> <span id="LC7319" 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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7146
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7320
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<pre style="margin: 0;"> <span id="LC7320" 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 unfold js-unfold old_line" data-linenumber="7230" style="width: 35px; color: rgba(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="7404" style="width: 35px; color: rgba(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">@@ -7230,9 +7404,6 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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7230
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<td class="new_line diff-line-num" data-linenumber="7404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7404
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<pre style="margin: 0;"> <span id="LC7404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_mhc_needed</span><span class="p">)</span> <span class="p">{</span></span>
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7231
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<td class="new_line diff-line-num" data-linenumber="7405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7405
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<pre style="margin: 0;"> <span id="LC7405" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_write_mhc</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;">write_mhcraw_cacheline_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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7232
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7406
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<pre style="margin: 0;"> <span id="LC7406" class="line" lang="cpp"> <span class="p">}</span></span>
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7233
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<td class="new_line diff-line-num old" data-linenumber="7407" style="width: 35px; color: rgba(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="LC7233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">write_mhc_needed</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="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="old_line diff-line-num old" data-linenumber="7234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7234
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<td class="new_line diff-line-num old" data-linenumber="7407" style="width: 35px; color: rgba(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="LC7234" class="line" lang="cpp"> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">thread_cumulative_popcount_bufs</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;">uint32_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;">Int32CtToCachelineCt</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;">kCacheline</span><span class="p">));</span></span>
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7235
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<pre style="margin: 0;">-<span id="LC7235" class="line" lang="cpp"> <span class="p">}</span></span>
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7236
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7407
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<pre style="margin: 0;"> <span id="LC7407" class="line" lang="cpp"> <span class="p">}</span></span>
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7237
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7408
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<pre style="margin: 0;"> <span id="LC7408" class="line" lang="cpp"> <span class="p">}</span></span>
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7238
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7409
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<pre style="margin: 0;"> <span id="LC7409" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</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 unfold js-unfold old_line" data-linenumber="7786" style="width: 35px; color: rgba(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="7957" style="width: 35px; color: rgba(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">@@ -7786,14 +7957,17 @@ PglErr WritePvarResorted(const char* outname, const uintptr_t* variant_include,</td>
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7786
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7957
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<pre style="margin: 0;"> <span id="LC7957" 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_variant_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;">raw_variant_ct</span><span class="p">);</span></span>
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7787
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7958
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<pre style="margin: 0;"> <span id="LC7958" 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;">all_nonref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nonref_flags_storage</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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7788
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<td class="new_line diff-line-num" data-linenumber="7959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7959
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<pre style="margin: 0;"> <span id="LC7959" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_nonref</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7789
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<td class="new_line diff-line-num old" data-linenumber="7960" style="width: 35px; color: rgba(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="LC7789" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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7960
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<pre style="margin: 0;">+<span id="LC7960" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_info_reload</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;">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="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7961
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<pre style="margin: 0;">+<span id="LC7961" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_info_reload</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="new_line diff-line-num new" data-linenumber="7962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7962
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<pre style="margin: 0;">+<span id="LC7962" class="line" lang="cpp"> <span class="p">}</span></span>
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7963
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<pre style="margin: 0;">+<span id="LC7963" 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;">write_info</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;">kfPvarColInfo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">;</span></span>
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7790
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7964
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<pre style="margin: 0;"> <span id="LC7964" 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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nonref_flags</span><span class="p">)</span> <span class="p">{</span></span>
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7791
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<td class="new_line diff-line-num" data-linenumber="7965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7965
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<pre style="margin: 0;"> <span id="LC7965" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</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;">nonref_flags</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="old_line diff-line-num" data-linenumber="7792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7792
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7966
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<pre style="margin: 0;"> <span id="LC7966" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="7793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7793
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<td class="new_line diff-line-num" data-linenumber="7967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7967
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<pre style="margin: 0;"> <span id="LC7967" class="line" lang="cpp"> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_info_pr</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">write_info</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="7794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7794
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<td class="new_line diff-line-num" data-linenumber="7968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7968
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<pre style="margin: 0;"> <span id="LC7968" 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;">write_info_pr</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;">kfInfoPrNonflagPresent</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="7795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7795
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<td class="new_line diff-line-num" data-linenumber="7969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7969
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<pre style="margin: 0;"> <span id="LC7969" 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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<td class="old_line diff-line-num old" data-linenumber="7796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7796
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<td class="new_line diff-line-num old" data-linenumber="7970" style="width: 35px; color: rgba(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="LC7796" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"><span class="idiff left">'</span>provisional reference<span class="idiff right">'</span> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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="new_line diff-line-num new" data-linenumber="7970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7970
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<pre style="margin: 0;">+<span id="LC7970" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting INFO/PR definitions. Either fix all REF alleles so that the</span><span class="se" style="color: #d14;">\n<span class="idiff left">\"</span></span><span class="s" style="color: #d14;">provisional reference</span><span class="se" style="color: #d14;"><span class="idiff right">\"</span></span><span class="s" style="color: #d14;"> flag is no longer needed, or remove/rename the other</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">use of the INFO/PR key.</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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7797
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7971
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<pre style="margin: 0;"> <span id="LC7971" 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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7798
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<td class="new_line diff-line-num" data-linenumber="7972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7972
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<pre style="margin: 0;"> <span id="LC7972" class="line" lang="cpp"> <span class="p">}</span></span>
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7799
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<td class="new_line diff-line-num" data-linenumber="7973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7973
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<pre style="margin: 0;"> <span id="LC7973" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#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">@@ -71,13 +71,14 @@ CONSTI32(kMaxInfoKeySlen, kMaxIdSlen);</td>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_INFO_KEY_SLEN_STR MAX_ID_SLEN_STR</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// We only need to distinguish between the following INFO-value-type cases:</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Number=0 (flag), Number=<positive integer>, Number=., Number=A, Number=R,</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// and Number=G. We use negative numbers to represent the last 4 cases in</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Number=0 (flag), Number=<positive integer>, Number=., Number=A, and</span></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;">// Number=R. (Number=G is being treated as Number=., since otherwise chrX is a</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;">// nightmare; see https://github.com/samtools/hts-specs/issues/272 for some</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// discussion.) We use negative numbers to represent the last 3 cases in</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// InfoVtype.</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="n" style="color: #333;">CONSTI32</span><span class="p">(</span><span class="n" style="color: #333;">kInfoVtypeUnknown</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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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="n" style="color: #333;">CONSTI32</span><span class="p">(</span><span class="n" style="color: #333;">kInfoVtypeA</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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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="n" style="color: #333;">CONSTI32</span><span class="p">(</span><span class="n" style="color: #333;">kInfoVtypeR</span><span class="p">,</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="LC80" class="line" lang="cpp"><span class="n" style="color: #333;">CONSTI32</span><span class="p">(</span><span class="n" style="color: #333;">kInfoVtypeG</span><span class="p">,</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="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Main fixed data structure when splitting/joining INFO is a hashmap of keys.</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Behavior when splitting:</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">@@ -87,17 +88,15 @@ CONSTI32(kInfoVtypeG, -4);</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=A and Number=R require splitting the value on ',' and verifying the</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// comma count is correct, but is otherwise straightforward since alleles</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// can't be permuted.</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=G requires a bit more work but isn't fundamentally different from</span></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;">// A/R.</span></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;">// - Number=G is being treated as Number=.</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// When joining:</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Field order is determined by header line order.</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=. and Number>0 just require a buffer of size ~info_reload_slen,<span class="idiff left right"> and</span></span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// a boolean indicating whether no mismatch has been found.</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=.<span class="idiff left right">/G</span> and Number>0 just require a buffer of size ~info_reload_slen,</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">and </span>a boolean indicating whether no mismatch has been found.</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=0 (Flag) requires a single boolean, we perform an or operation.</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=A/R<span class="idiff left right">/G</span> are the messy ones: we need to have enough space for</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Number=A/R are the messy ones: we need to have enough space for</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// max_write_allele_ct (or that minus 1) comma-separated values in the =A and</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// =R cases, and max_write_allele_ct * (max_write_allele_ct + 1) / 2 in the</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// diploid =G case.</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// =R cases.</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Since we permit already-multiallelic variants to be part of a join, the =G</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// case may require a lot of working memory to handle. We reserve up to 1/16</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// of remaining workspace memory for this when we cannot prove that we can</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">@@ -136,6 +135,14 @@ uint32_t DataParentalColsAreRequired(const uintptr_t* sample_include, const Samp</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC136" 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;">AppendPhenoStr</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_col</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;">output_missing_pheno</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">omp_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_uidx</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</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndPermute8bit</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="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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">val_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="LC139" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">CopyAndPermute16bit</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="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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">old_sample_idx_to_new</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;">val_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="LC142" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Dense8bitToSparse</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;">set</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ctl</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;">vals</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Dense16bitToSparse</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;">set</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ctl</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;">vals</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">LoadAlleleAndGenoCounts</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="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">founder_info</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="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;">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="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;">founder_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">male_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nosex_ct</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;">first_hap_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_minimac3_r2</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="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="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="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="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_ddosages</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="n" style="color: #333;">founder_allele_ddosages</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;">variant_missing_hc_cts</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;">variant_missing_dosage_cts</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;">variant_hethap_cts</span><span class="p">,</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">raw_geno_cts</span><span class="p">),</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">founder_raw_geno_cts</span><span class="p">),</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">x_male_geno_cts</span><span class="p">),</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">founder_x_male_geno_cts</span><span class="p">),</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">x_nosex_geno_cts</span><span class="p">),</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">founder_x_nosex_geno_cts</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;">imp_r2_vals</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ApplyHardCallThresh</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>
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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">@@ -964,6 +964,7 @@ PglErr ExportOxGen(const uintptr_t* sample_include, const uint32_t* sample_inclu</td>
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="cpp"> <span class="p">}</span></span>
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"> <span class="p">}</span></span>
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966
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966
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<pre style="margin: 0;"> <span id="LC966" 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;">max_chr_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetMaxChrSlen</span><span class="p">(</span><span class="n" style="color: #333;">cip</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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<pre style="margin: 0;">+<span id="LC967" 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_v2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">exportf_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfExportfOxGenV2</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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967
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if no dosages, all genotypes are 6 bytes (missing = " 0 0 0")</span></span>
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968
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// with dosages, we print up to 5 digits past the decimal point, so 7 bytes</span></span>
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969
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// + space for each number, 24 bytes max</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">@@ -971,7 +972,7 @@ PglErr ExportOxGen(const uintptr_t* sample_include, const uint32_t* sample_inclu</td>
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971
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972
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<pre style="margin: 0;"> <span id="LC972" 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_buf</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// includes trailing space</span></span>
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972
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973
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<pre style="margin: 0;"> <span id="LC973" 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;">writebuf</span><span class="p">;</span></span>
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973
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974
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<pre style="margin: 0;"> <span id="LC974" 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_c</span><span class="p">(</span><span class="n" style="color: #333;">max_chr_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chr_buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">kMaxMediumLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_chr_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kMaxIdSlen</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="mi" style="color: #099;">2</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;">max_geno_slen</span> <span class="o" style="font-weight: 600;">*</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;">writebuf</span><span class="p">)))</span> <span class="p">{</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">kMaxMediumLine</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_chr_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">kMaxIdSlen</span> <span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_v2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </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="mi" style="color: #099;">2</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;">max_geno_slen</span> <span class="o" style="font-weight: 600;">*</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;">writebuf</span><span class="p">)))</span> <span class="p">{</span></span>
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975
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ExportOxGen_ret_NOMEM</span><span class="p">;</span></span>
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976
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="cpp"> <span class="p">}</span></span>
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977
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978
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<pre style="margin: 0;"> <span id="LC978" 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="1035" style="width: 35px; color: rgba(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="1036" style="width: 35px; color: rgba(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">@@ -1035,7 +1036,12 @@ PglErr ExportOxGen(const uintptr_t* sample_include, const uint32_t* sample_inclu</td>
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1035
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="cpp"> <span class="n" style="color: #333;">is_y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chr_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y_code</span><span class="p">);</span></span>
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1036
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="cpp"> <span class="p">}</span></span>
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1037
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1038
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<pre style="margin: 0;"> <span id="LC1038" 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;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">chr_blen</span><span class="p">);</span></span>
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1038
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<pre style="margin: 0;">-<span id="LC1038" 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;">strcpyax</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="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" 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;">variant_id</span> <span class="o" style="font-weight: 600;">=</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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1040
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<pre style="margin: 0;">+<span id="LC1040" 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;">variant_id_slen</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;">variant_id</span><span class="p">);</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" 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;">memcpyax</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_id</span><span class="p">,</span> <span class="n" style="color: #333;">variant_id_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_v2</span><span class="p">)</span> <span class="p">{</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" 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;">memcpyax</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_id</span><span class="p">,</span> <span class="n" style="color: #333;">variant_id_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="p">}</span></span>
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1039
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1045
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<pre style="margin: 0;"> <span id="LC1045" 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;">u32toa_x</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_uidx</span><span class="p">],</span> <span class="sc" style="color: #d14;">' '</span><span class="p">,</span> <span class="n" style="color: #333;">write_iter</span><span class="p">);</span></span>
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1040
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1046
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<pre style="margin: 0;"> <span id="LC1046" 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;">variant_uidx</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1041
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1047
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<pre style="margin: 0;"> <span id="LC1047" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3158,12 +3164,13 @@ THREAD_FUNC_DECL ExportBgen13Thread(void* raw_arg) {</td>
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3158
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3164
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<pre style="margin: 0;"> <span id="LC3164" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// export an ID hash table as well (since such a hash table is always</span></span>
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3159
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3165
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<pre style="margin: 0;"> <span id="LC3165" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// constructed for the sake of detecting and warning about duplicate</span></span>
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3160
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3166
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<pre style="margin: 0;"> <span id="LC3166" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// post-id-paste IDs).</span></span>
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3161
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<pre style="margin: 0;">-<span id="LC3161" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ExportIdpaste</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;">ftypename</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;">IdpasteFlags</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">exportf_id_delim</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;">max_exported_sample_id_blen_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;">exported_sample_ids_ptr</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="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ExportIdpaste</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;">ftypename</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">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">reimport_flagname</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;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">IdpasteFlags</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">exportf_id_delim</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;">max_exported_sample_id_blen_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;">exported_sample_ids_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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3162
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3168
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<pre style="margin: 0;"> <span id="LC3168" 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;">write_fid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataFidColIsRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfIdpasteMaybefid</span><span class="p">);</span></span>
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3163
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3169
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<pre style="margin: 0;"> <span id="LC3169" 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;">sample_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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3164
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3170
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<pre style="margin: 0;"> <span id="LC3170" 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;">sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">;</span></span>
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3165
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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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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3166
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3172
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<pre style="margin: 0;"> <span id="LC3172" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3173
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<pre style="margin: 0;">+<span id="LC3173" 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;">write_iid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">exportf_id_paste</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfIdpasteIid</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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3167
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<td class="new_line diff-line-num" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3174
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<pre style="margin: 0;"> <span id="LC3174" 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;">write_sid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSidColIsRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfIdpasteMaybesid</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3168
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<td class="new_line diff-line-num" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3175
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<pre style="margin: 0;"> <span id="LC3175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_sid</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;">sids</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="3169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3169
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<td class="new_line diff-line-num" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3176
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<pre style="margin: 0;"> <span id="LC3176" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sid_blen</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 unfold js-unfold old_line" data-linenumber="3194" style="width: 35px; color: rgba(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="3201" style="width: 35px; color: rgba(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">@@ -3194,7 +3201,7 @@ BoolErr ExportIdpaste(const uintptr_t* sample_include, const SampleIdInfo* siip,</td>
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3194
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3201
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<pre style="margin: 0;"> <span id="LC3201" class="line" lang="cpp"> <span class="p">}</span></span>
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3195
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<td class="new_line diff-line-num" data-linenumber="3202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3202
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<pre style="margin: 0;"> <span id="LC3202" class="line" lang="cpp"> <span class="n" style="color: #333;">exported_sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">exported_sample_ids_iter</span><span class="p">,</span> <span class="n" style="color: #333;">orig_sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">fid_slen</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3196
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<td class="new_line diff-line-num" data-linenumber="3203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3203
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<pre style="margin: 0;"> <span id="LC3203" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3197
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<td class="new_line diff-line-num old" data-linenumber="3204" style="width: 35px; color: rgba(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="LC3197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">exportf_id_paste</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">kfIdpasteI</span>id</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3198" style="width: 35px; color: rgba(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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3204
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<pre style="margin: 0;">+<span id="LC3204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">write_i</span>id</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="3198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3198
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3205
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<pre style="margin: 0;"> <span id="LC3205" 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;">orig_iid</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;">orig_fid_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3199
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<td class="new_line diff-line-num" data-linenumber="3206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3206
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<pre style="margin: 0;"> <span id="LC3206" 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;">iid_slen</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;">orig_iid</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="3200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3200
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<td class="new_line diff-line-num" data-linenumber="3207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3207
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<pre style="margin: 0;"> <span id="LC3207" 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;">id_delim_warning</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">memchr</span><span class="p">(</span><span class="n" style="color: #333;">orig_iid</span><span class="p">,</span> <span class="n" style="color: #333;">id_delim</span><span class="p">,</span> <span class="n" style="color: #333;">iid_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="3217" style="width: 35px; color: rgba(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="3224" style="width: 35px; color: rgba(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">@@ -3217,12 +3224,11 @@ BoolErr ExportIdpaste(const uintptr_t* sample_include, const SampleIdInfo* siip,</td>
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3217
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<td class="new_line diff-line-num" data-linenumber="3224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3224
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<pre style="margin: 0;"> <span id="LC3224" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3218
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<td class="new_line diff-line-num" data-linenumber="3225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3225
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<pre style="margin: 0;"> <span id="LC3225" class="line" lang="cpp"> <span class="n" style="color: #333;">exported_sample_ids_iter</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="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3219
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<td class="new_line diff-line-num" data-linenumber="3226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3226
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<pre style="margin: 0;"> <span id="LC3226" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3220
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<td class="new_line diff-line-num old" data-linenumber="3227" style="width: 35px; color: rgba(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="LC3220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// todo: revise this warning condition?</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3221
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<td class="new_line diff-line-num old" data-linenumber="3227" style="width: 35px; color: rgba(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="LC3221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">id_delim_warning</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3222" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="3227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3227
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<pre style="margin: 0;">+<span id="LC3227" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">id_delim_warning</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">write_fid</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">write_iid</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">write_sid</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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3222
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3228
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<pre style="margin: 0;"> <span id="LC3228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exportf_id_delim</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3223
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<td class="new_line diff-line-num old" data-linenumber="3229" style="width: 35px; color: rgba(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="LC3223" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: '%c' present in original sample IDs; --<span class="idiff left">export </span>%s will not be able to reconstruct them. Consider rerunning with a different --export id-delim= value.</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;">exportf_id_delim</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff right">ftype</span>name</span><span class="p">);</span></span>
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3229
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<pre style="margin: 0;">+<span id="LC3229" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: '%c' present in original sample IDs; --%s will not be able to reconstruct them. Consider rerunning with a different --export id-delim= value.</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;">exportf_id_delim</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">reimport_flag</span>name</span><span class="p">);</span></span>
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3224
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<td class="new_line diff-line-num" data-linenumber="3230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3230
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<pre style="margin: 0;"> <span id="LC3230" 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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3225
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<pre style="margin: 0;">-<span id="LC3225" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: '_' present in original sample IDs; --<span class="idiff left">export </span>%s will not be able to reconstruct them. Consider rerunning with a suitable --export id-delim= value.</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;"><span class="idiff right">ftype</span>name</span><span class="p">);</span></span>
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3231
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<pre style="margin: 0;">+<span id="LC3231" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: '_' present in original sample IDs; --%s will not be able to reconstruct them. Consider rerunning with a suitable --export id-delim= value.</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;"><span class="idiff left right">reimport_flag</span>name</span><span class="p">);</span></span>
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3226
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3232
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<pre style="margin: 0;"> <span id="LC3232" class="line" lang="cpp"> <span class="p">}</span></span>
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3227
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3233
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<pre style="margin: 0;"> <span id="LC3233" class="line" lang="cpp"> <span class="p">}</span></span>
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3228
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3234
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<pre style="margin: 0;"> <span id="LC3234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PopulateStrboxHtable</span><span class="p">(</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="n" style="color: #333;">exported_id_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">new_id_htable</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="3333" style="width: 35px; color: rgba(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="3339" style="width: 35px; color: rgba(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">@@ -3333,7 +3339,7 @@ PglErr ExportBgen13(const char* outname, const uintptr_t* sample_include, uint32</td>
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3333
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3339
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<pre style="margin: 0;"> <span id="LC3339" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// always save sample IDs...</span></span>
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3334
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3340
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<pre style="margin: 0;"> <span id="LC3340" 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;">exported_sample_ids</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3335
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<td class="new_line diff-line-num" data-linenumber="3341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3341
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<pre style="margin: 0;"> <span id="LC3341" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3336
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<td class="new_line diff-line-num old" data-linenumber="3342" style="width: 35px; color: rgba(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="LC3336" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="n" style="color: #333;">use_zstd_compression</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"bgen-1.3"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"bgen-1.2"</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3337" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="3342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3342
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<pre style="margin: 0;">+<span id="LC3342" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="n" style="color: #333;">use_zstd_compression</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"bgen-1.3"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"bgen-1.2"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"bgen"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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3337
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<td class="new_line diff-line-num" data-linenumber="3343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3343
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<pre style="margin: 0;"> <span id="LC3343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ExportBgen13_ret_NOMEM</span><span class="p">;</span></span>
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3338
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3344
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<pre style="margin: 0;"> <span id="LC3344" class="line" lang="cpp"> <span class="p">}</span></span>
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3339
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3345
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<pre style="margin: 0;"> <span id="LC3345" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Compute total length of sample ID block now; this is necessary to fill</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3898" style="width: 35px; color: rgba(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="3904" style="width: 35px; color: rgba(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">@@ -3898,7 +3904,7 @@ PglErr ExportOxSampleV2(const char* outname, const uintptr_t* sample_include, co</td>
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3898
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3904
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<pre style="margin: 0;"> <span id="LC3904" class="line" lang="cpp"></span>
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3899
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<td class="new_line diff-line-num" data-linenumber="3905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3905
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<pre style="margin: 0;"> <span id="LC3905" 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;">exported_sample_ids</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3900
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<td class="new_line diff-line-num" data-linenumber="3906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3906
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<pre style="margin: 0;"> <span id="LC3906" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="3901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3901
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<td class="new_line diff-line-num old" data-linenumber="3907" style="width: 35px; color: rgba(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="LC3901" 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;">ExportIdpaste</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;">piip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sii</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-v2"</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="3902" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="3907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3907
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<pre style="margin: 0;">+<span id="LC3907" 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;">ExportIdpaste</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;">piip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sii</span><span class="p">,</span> <span class="s" style="color: #d14;">"sample-v2"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"sample"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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3902
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<td class="new_line diff-line-num" data-linenumber="3908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3908
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<pre style="margin: 0;"> <span id="LC3908" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ExportOxSampleV2_ret_NOMEM</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="3903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3903
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<td class="new_line diff-line-num" data-linenumber="3909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3909
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<pre style="margin: 0;"> <span id="LC3909" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="3904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3904
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<td class="new_line diff-line-num" data-linenumber="3910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3910
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<pre style="margin: 0;"> <span id="LC3910" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4607" style="width: 35px; color: rgba(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="4613" style="width: 35px; color: rgba(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">@@ -4607,7 +4613,7 @@ PglErr ExportVcf(const uintptr_t* sample_include, const uint32_t* sample_include</td>
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<td class="old_line diff-line-num" data-linenumber="4607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4607
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<td class="new_line diff-line-num" data-linenumber="4613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4613
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4613" 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;">"##FORMAT=<ID=GT,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Genotype</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="s" style="color: #d14;">"#CHROM</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">POS</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ALT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">QUAL</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FILTER</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">INFO</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">FORMAT"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="4608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4608
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<td class="new_line diff-line-num" data-linenumber="4614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4614
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<pre style="margin: 0;"> <span id="LC4614" 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;">exported_sample_ids</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4609
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<td class="new_line diff-line-num" data-linenumber="4615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4615
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<pre style="margin: 0;"> <span id="LC4615" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4610
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<td class="new_line diff-line-num old" data-linenumber="4616" style="width: 35px; color: rgba(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="LC4610" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="s" style="color: #d14;">"vcf"</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="4611" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="4616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4616
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<pre style="margin: 0;">+<span id="LC4616" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="s" style="color: #d14;">"vcf"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"vcf"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4611
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<td class="new_line diff-line-num" data-linenumber="4617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4617
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<pre style="margin: 0;"> <span id="LC4617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ExportVcf_ret_NOMEM</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="4612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4612
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<td class="new_line diff-line-num" data-linenumber="4618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4618
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<pre style="margin: 0;"> <span id="LC4618" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="4613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4613
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<td class="new_line diff-line-num" data-linenumber="4619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4619
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4619" 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;">sample_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;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">sample_idx</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="7976" style="width: 35px; color: rgba(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="7982" style="width: 35px; color: rgba(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">@@ -7976,7 +7982,7 @@ PglErr ExportBcf(const uintptr_t* sample_include, const uint32_t* sample_include</td>
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7982
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<pre style="margin: 0;"> <span id="LC7982" class="line" lang="cpp"></span>
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7977
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7983
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<pre style="margin: 0;"> <span id="LC7983" 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;">exported_sample_ids</span><span class="p">;</span></span>
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7978
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7984
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<pre style="margin: 0;"> <span id="LC7984" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">;</span></span>
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7979
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<pre style="margin: 0;">-<span id="LC7979" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcf"</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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7985
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<pre style="margin: 0;">+<span id="LC7985" 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;">ExportIdpaste</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="s" style="color: #d14;">"bcf"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"bcf"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_paste</span><span class="p">,</span> <span class="n" style="color: #333;">exportf_id_delim</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_exported_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exported_sample_ids</span><span class="p">)))</span> <span class="p">{</span></span>
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7980
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7986
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<pre style="margin: 0;"> <span id="LC7986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ExportBcf_ret_NOMEM</span><span class="p">;</span></span>
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7987
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<pre style="margin: 0;"> <span id="LC7987" class="line" lang="cpp"> <span class="p">}</span></span>
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7982
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7988
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<pre style="margin: 0;"> <span id="LC7988" 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;">sample_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;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</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;">sample_idx</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="542" style="width: 35px; color: rgba(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">@@ -542,7 +542,8 @@ PglErr ProcessFa(const uintptr_t* variant_include, const char* const* variant_id</td>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ucc</span> <span class="o" style="font-weight: 600;"><</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// > = ascii 62</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ; = ascii 59</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ucc</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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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (25 May 2021): newline is also valid</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ucc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">';'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">ucc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ucc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">is_first_noncomment_line</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4383,7 +4383,9 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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4383
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<pre style="margin: 0;"> <span id="LC4383" class="line" lang=""> ZeromovFArr(nm_sample_ct_rem, &nm_predictors_pmaj_iter);</span>
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4384
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4384
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<pre style="margin: 0;"> <span id="LC4384" class="line" lang=""> }</span>
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4385
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4385
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<pre style="margin: 0;"> <span id="LC4385" class="line" lang=""> nm_predictors_pmaj_istart = nm_predictors_pmaj_iter;</span>
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4386
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<pre style="margin: 0;">-<span id="LC4386" class="line" lang=""> prev_nm = !missing_ct;</span>
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4386
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<pre style="margin: 0;">+<span id="LC4386" class="line" lang=""> // bugfix (13 Apr 2021): if local covariates are present, we can't</span>
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4387
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<pre style="margin: 0;">+<span id="LC4387" class="line" lang=""> // optimize as aggressively</span>
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4388
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<pre style="margin: 0;">+<span id="LC4388" class="line" lang=""> prev_nm = !(missing_ct || local_covar_ct);</span>
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4387
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4389
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<pre style="margin: 0;"> <span id="LC4389" class="line" lang=""> } else {</span>
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4388
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4390
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<pre style="margin: 0;"> <span id="LC4390" class="line" lang=""> // bugfix (15 Aug 2018): this was not handling --parameters</span>
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4389
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4391
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<pre style="margin: 0;"> <span id="LC4391" class="line" lang=""> // correctly when a covariate was only needed as part of an</span>
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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7436,7 +7438,7 @@ THREAD_FUNC_DECL GlmLinearThread(void* raw_arg) {</td>
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7436
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7438
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<pre style="margin: 0;"> <span id="LC7438" class="line" lang=""> }</span>
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7437
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7439
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<pre style="margin: 0;"> <span id="LC7439" class="line" lang=""> }</span>
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7438
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7440
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<pre style="margin: 0;"> <span id="LC7440" class="line" lang=""> nm_predictors_pmaj_istart = nm_predictors_pmaj_iter;</span>
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7439
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<pre style="margin: 0;">-<span id="LC7439" class="line" lang=""> prev_nm = !missing_ct;</span>
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<pre style="margin: 0;">+<span id="LC7441" class="line" lang=""> prev_nm = !<span class="idiff left">(</span>missing_ct<span class="idiff right"> || local_covar_ct)</span>;</span>
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7440
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7442
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<pre style="margin: 0;"> <span id="LC7442" class="line" lang=""> } else {</span>
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7441
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7443
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<pre style="margin: 0;"> <span id="LC7443" class="line" lang=""> // bugfix (15 Aug 2018): this was not handling --parameters</span>
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7442
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7444
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<pre style="margin: 0;"> <span id="LC7444" class="line" lang=""> // correctly when a covariate was only needed as part of an</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">@@ -9504,7 +9506,7 @@ THREAD_FUNC_DECL GlmLinearSubbatchThread(void* raw_arg) {</td>
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9504
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9506
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<pre style="margin: 0;"> <span id="LC9506" class="line" lang=""> }</span>
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9505
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9507
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<pre style="margin: 0;"> <span id="LC9507" class="line" lang=""> }</span>
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9506
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9508
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<pre style="margin: 0;"> <span id="LC9508" class="line" lang=""> nm_predictors_pmaj_istart = nm_predictors_pmaj_iter;</span>
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9507
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<pre style="margin: 0;">-<span id="LC9507" class="line" lang=""> prev_nm = !missing_ct;</span>
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9509
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<pre style="margin: 0;">+<span id="LC9509" class="line" lang=""> prev_nm = !<span class="idiff left">(</span>missing_ct<span class="idiff right"> || local_covar_ct)</span>;</span>
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9508
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9510
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<pre style="margin: 0;"> <span id="LC9510" class="line" lang=""> } else {</span>
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9509
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9511
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<pre style="margin: 0;"> <span id="LC9511" class="line" lang=""> // bugfix (15 Aug 2018): this was not handling --parameters</span>
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9512
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<pre style="margin: 0;"> <span id="LC9512" class="line" lang=""> // correctly when a covariate was only needed as part of an</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">@@ -11140,6 +11142,8 @@ PglErr GlmMain(const uintptr_t* orig_sample_include, const SampleIdInfo* siip, c</td>
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11140
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11142
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<pre style="margin: 0;"> <span id="LC11142" class="line" lang=""> if (new_max_covar_name_blen < condition_blen) {</span>
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11143
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<pre style="margin: 0;"> <span id="LC11143" class="line" lang=""> new_max_covar_name_blen = condition_blen;</span>
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11144
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<pre style="margin: 0;"> <span id="LC11144" class="line" lang=""> }</span>
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<pre style="margin: 0;">+<span id="LC11145" class="line" lang=""> // TODO: this count will be different with a multiallelic variant</span>
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<pre style="margin: 0;">+<span id="LC11146" class="line" lang=""> logprintf("--glm: One --condition covariate added.\n");</span>
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11147
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<pre style="margin: 0;"> <span id="LC11147" class="line" lang=""> } else {</span>
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11148
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<pre style="margin: 0;"> <span id="LC11148" class="line" lang=""> if (unlikely(ii == -2)) {</span>
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11149
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<pre style="margin: 0;"> <span id="LC11149" class="line" lang=""> logerrprintfww("Error: Duplicate --condition variant ID '%s'.\n", glm_info_ptr->condition_varname);</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">@@ -463,8 +463,12 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is 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="LC464" class="line" lang="cpp"><span class="s" style="color: #d14;">" genotype-based list which omits the most common genotype for</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="LC465" class="line" lang="cpp"><span class="s" style="color: #d14;">" each variant. Also supports 'omit-nonmale-y'.</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="LC466" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier 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="LC467" class="line" lang="cpp"><span class="s" style="color: #d14;">" present, the .gen file is 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="LC466" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'oxford', 'oxford-v2': Oxford-format .gen + .sample. When the 'bgz'</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="LC467" class="line" lang="cpp"><span class="s" style="color: #d14;">" modifier is present, the .gen 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="LC468" class="line" lang="cpp"><span class="s" style="color: #d14;">" block-gzipped. 'oxford' requests the original</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;">" .gen file format with 5 leading columns</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;">" (understood by older PLINK builds); 'oxford-v2'</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;">" requests the current 6-leading-column flavor.</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;">" * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'compound-genotypes': Same as 'ped', except that the space between each</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"><span class="s" style="color: #d14;">" pair of same-variant allele codes is removed.</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">@@ -1311,8 +1315,8 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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1311
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="cpp"><span class="s" style="color: #d14;">" scoresums: Score sums.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1312
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"><span class="s" style="color: #d14;">" The default is maybefid,maybesid,phenos,nallele,dosagesum,scoreavgs.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1313
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1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="cpp"><span class="s" style="color: #d14;">" For more sophisticated polygenic risk scoring, we recommend looking at the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1314
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="cpp"><span class="s" style="color: #d14;">" LDpred (https://<span class="idiff left right">github.com/bvilhjal/ldpred ) and PRSice-2</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="LC1315" class="line" lang="cpp"><span class="s" style="color: #d14;">" (https://www.prsice.info/ ) software packages.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="cpp"><span class="s" style="color: #d14;">" LDpred<span class="idiff left">2</span> (https://<span class="idiff right">privefl.github.io/bigsnpr/articles/LDpred2.html ) and</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="LC1319" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">PRSice-2 </span>(https://www.prsice.info/ ) software packages.</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"variant-score</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">vscore</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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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="cpp"><span class="s" style="color: #d14;">" --variant-score <filename> ['bin' | 'bin4' | 'cols='<col set descriptor>]</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">@@ -1715,9 +1719,9 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="cpp"><span class="s" style="color: #d14;">" Linearly transform named covariates (and quantitative phenotypes, if</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="LC1720" class="line" lang="cpp"><span class="s" style="color: #d14;">" --variance-standardize) to mean-zero, variance 1. If no arguments are</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1721
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="cpp"><span class="s" style="color: #d14;">" provided, all possible phenotypes/covariates are affected.</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="LC1718" class="line" lang="cpp"><span class="s" style="color: #d14;">" This is frequently necessary to prevent multicollinearity <span class="idiff left">w</span>he<span class="idiff right">n dealing with</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="LC1719" class="line" lang="cpp"><span class="s" style="color: #d14;">" covariates where abs(mean) is much larger than<span class="idiff left right"> abs(standard deviation),</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="LC1720" class="line" lang="cpp"><span class="s" style="color: #d14;">" such as year of birth.</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="LC1722" class="line" lang="cpp"><span class="s" style="color: #d14;">" This is frequently necessary to prevent <span class="idiff left">the </span>multicollinearity <span class="idiff">c</span>he<span class="idiff right">ck from</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="LC1723" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">failing when dealing with </span>covariates where abs(mean) is much larger than</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1724
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<pre style="margin: 0;">+<span id="LC1724" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">the standard deviation, </span>such as year of birth.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1721
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1725
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<pre style="margin: 0;"> <span id="LC1725" class="line" lang="cpp"><span class="s" style="color: #d14;">" --quantile-normalize [...] : Force named covariates and quantitative</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1722
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1726
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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="cpp"><span class="s" style="color: #d14;">" --pheno-quantile-normalize [...] phenotypes to a N(0,1) distribution,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1723
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1727
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="cpp"><span class="s" style="color: #d14;">" --covar-quantile-normalize [...] preserving only the original rank orders.</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="2118" style="width: 35px; color: rgba(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="2122" style="width: 35px; color: rgba(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">@@ -2118,7 +2122,9 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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2118
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2122
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<pre style="margin: 0;"> <span id="LC2122" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'file'/'f' uses the order in the given file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2119
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2123
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="cpp"><span class="s" style="color: #d14;">" (named in the last argument).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2120
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2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="cpp"> <span class="p">);</span></span>
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2121
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<td class="new_line diff-line-num old" data-linenumber="2125" style="width: 35px; color: rgba(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="LC2121" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"pmerge</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-list</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">sample-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">variant-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pheno-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-parents-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-sex-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-pheno-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-xheader-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-qual-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-filter-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-info-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-cm-mode</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;">0</span><span class="p">,</span></span>
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2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"pmerge</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-list</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-list-dir</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-output-vzs</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">sample-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">variant-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pheno-inner-join</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-parents-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-sex-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-pheno-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-xheader-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-qual-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-filter-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-info-mode</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-cm-mode</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;">0</span><span class="p">,</span></span>
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2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="cpp"><span class="s" style="color: #d14;">" --pmerge-list-dir <dir> : Specify base dir to join to --pmerge-list entries.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="cpp"><span class="s" style="color: #d14;">" --pmerge-output-vzs : Compress the .pvar file from --pmerge[-list].</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2122
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2128
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<pre style="margin: 0;"> <span id="LC2128" class="line" lang="cpp"><span class="s" style="color: #d14;">" --sample-inner-join : By default, --pmerge[-list] performs an 'outer</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2123
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2129
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<pre style="margin: 0;"> <span id="LC2129" class="line" lang="cpp"><span class="s" style="color: #d14;">" --variant-inner-join join': the merged fileset contains the union of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2124
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2130
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<pre style="margin: 0;"> <span id="LC2130" class="line" lang="cpp"><span class="s" style="color: #d14;">" --pheno-inner-join the samples in the input filesets, and ditto for</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="2142" style="width: 35px; color: rgba(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="2148" style="width: 35px; color: rgba(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">@@ -2142,9 +2148,11 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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2142
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2148
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<pre style="margin: 0;"> <span id="LC2148" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-filter-mode <m> QUAL/FILTER/INFO/CM entries.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2143
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2149
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<pre style="margin: 0;"> <span id="LC2149" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-info-mode <mode> * 'erase' = remove column</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2144
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2150
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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-cm-mode <mode> * 'nm-match' = nonmissing values must match</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="LC2145" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'nm-first' = keep first nonmissing (<span class="idiff left right">qual/</span>info/CM</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'nm-first' = keep first nonmissing (info/CM</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="cpp"><span class="s" style="color: #d14;">" default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2147
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2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'first' = keep first value, even if missing</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="LC2154" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'min' = keep minimum value (--merge-qual-mode</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="LC2155" class="line" lang="cpp"><span class="s" style="color: #d14;">" default, not applicable to others)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2148
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2156
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<pre style="margin: 0;"> <span id="LC2156" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'np-union' = keep all non-PASS values</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2149
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2157
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<pre style="margin: 0;"> <span id="LC2157" class="line" lang="cpp"><span class="s" style="color: #d14;">" (--merge-filter-mode default, not</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2158
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<pre style="margin: 0;"> <span id="LC2158" class="line" lang="cpp"><span class="s" style="color: #d14;">" applicable to others)</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">@@ -3119,7 +3119,7 @@ PglErr VcfToPgen(const char* vcfname, const char* preexisting_psamname, const ch</td>
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3119
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<pre style="margin: 0;"> <span id="LC3119" class="line" lang=""> allele_idx_end += alt_ct + 1;</span>
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3120
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<pre style="margin: 0;"> <span id="LC3120" class="line" lang=""> const uint32_t variant_idx_lowbits = variant_ct % kBitsPerWord;</span>
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3121
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<pre style="margin: 0;"> <span id="LC3121" class="line" lang=""> if (info_pr_present) {</span>
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<pre style="margin: 0;">-<span id="LC3122" class="line" lang=""> if (PrInInfo<span class="idiff left right">Token</span>(info_end - info_start, info_start)) {</span>
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3122
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<pre style="margin: 0;">+<span id="LC3122" class="line" lang=""> if (PrInInfo(info_end - info_start, info_start)) {</span>
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3123
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<pre style="margin: 0;"> <span id="LC3123" class="line" lang=""> nonref_word |= k1LU << variant_idx_lowbits;</span>
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3124
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<pre style="margin: 0;"> <span id="LC3124" class="line" lang=""> }</span>
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3125
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<pre style="margin: 0;"> <span id="LC3125" class="line" lang=""> if (variant_idx_lowbits == (kBitsPerWord - 1)) {</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">@@ -7881,65 +7881,68 @@ PglErr BcfToPgen(const char* bcfname, const char* preexisting_psamname, const ch</td>
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7881
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7881
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<pre style="margin: 0;"> <span id="LC7881" class="line" lang=""> }</span>
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7882
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<pre style="margin: 0;"> <span id="LC7882" class="line" lang=""> // INFO</span>
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7883
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7883
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<pre style="margin: 0;"> <span id="LC7883" class="line" lang=""> uintptr_t info_pr_here = 0;</span>
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7884
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<pre style="margin: 0;">-<span id="LC7884" class="line" lang=""> uint64_t cur_info_slen_ubound = n_info - 1;</span>
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7885
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<pre style="margin: 0;">-<span id="LC7885" class="line" lang=""> for (uint32_t uii = 0; uii != n_info; ++uii) {</span>
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7886
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<pre style="margin: 0;">-<span id="LC7886" class="line" lang=""> uint32_t sidx;</span>
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7887
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<pre style="margin: 0;">-<span id="LC7887" class="line" lang=""> if (unlikely(ScanBcfTypedInt(&parse_iter, &sidx) || (parse_iter > shared_end) || (sidx >= fif_string_idx_end))) {</span>
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7888
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<pre style="margin: 0;">-<span id="LC7888" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
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7889
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<pre style="margin: 0;">-<span id="LC7889" class="line" lang=""> }</span>
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7890
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<pre style="margin: 0;">-<span id="LC7890" class="line" lang=""> const uint32_t key_slen = fif_slens[sidx];</span>
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7891
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<pre style="margin: 0;">-<span id="LC7891" class="line" lang=""> if (unlikely((!key_slen) || ScanBcfType(&parse_iter, &value_type, &value_ct) || (parse_iter > shared_end))) {</span>
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7892
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<pre style="margin: 0;">-<span id="LC7892" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
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7893
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<pre style="margin: 0;">-<span id="LC7893" class="line" lang=""> }</span>
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7894
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<pre style="margin: 0;">-<span id="LC7894" class="line" lang=""> cur_info_slen_ubound += key_slen;</span>
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7895
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<pre style="margin: 0;">-<span id="LC7895" class="line" lang=""> if (value_ct) {</span>
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7896
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<pre style="margin: 0;">-<span id="LC7896" class="line" lang=""> const uint32_t bytes_per_elem = kBcfBytesPerElem[value_type];</span>
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7897
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<pre style="margin: 0;">-<span id="LC7897" class="line" lang=""> const uint64_t vec_byte_ct = bytes_per_elem * S_CAST(uint64_t, value_ct);</span>
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7898
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<pre style="margin: 0;">-<span id="LC7898" class="line" lang=""> if (unlikely((!bytes_per_elem) || (S_CAST(uint64_t, shared_end - parse_iter) < vec_byte_ct))) {</span>
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7884
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<pre style="margin: 0;">+<span id="LC7884" class="line" lang=""> if (n_info) {</span>
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7885
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<pre style="margin: 0;">+<span id="LC7885" class="line" lang=""> // bugfix (1 Jul 2021): avoid underflow when n_info == 0</span>
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7886
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<pre style="margin: 0;">+<span id="LC7886" class="line" lang=""> uint64_t cur_info_slen_ubound = n_info - 1;</span>
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7887
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<pre style="margin: 0;">+<span id="LC7887" class="line" lang=""> for (uint32_t uii = 0; uii != n_info; ++uii) {</span>
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7888
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<pre style="margin: 0;">+<span id="LC7888" class="line" lang=""> uint32_t sidx;</span>
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7889
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<pre style="margin: 0;">+<span id="LC7889" class="line" lang=""> if (unlikely(ScanBcfTypedInt(&parse_iter, &sidx) || (parse_iter > shared_end) || (sidx >= fif_string_idx_end))) {</span>
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7899
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7890
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<pre style="margin: 0;"> <span id="LC7890" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
</pre>
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7900
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7891
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<pre style="margin: 0;"> <span id="LC7891" class="line" lang=""> }</span>
</pre>
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7901
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<pre style="margin: 0;">-<span id="LC7901" class="line" lang=""> if (value_type == 1) {</span>
</pre>
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7902
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<pre style="margin: 0;">-<span id="LC7902" class="line" lang=""> // int8, max len 4 ("-127"), add 1 for comma</span>
</pre>
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7903
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<pre style="margin: 0;">-<span id="LC7903" class="line" lang=""> cur_info_slen_ubound += 5 * S_CAST(uint64_t, value_ct);</span>
</pre>
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7904
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<pre style="margin: 0;">-<span id="LC7904" class="line" lang=""> } else if (value_type == 2) {</span>
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7905
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<pre style="margin: 0;">-<span id="LC7905" class="line" lang=""> // int16, max len 6</span>
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7906
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7906" class="line" lang=""> cur_info_slen_ubound += 7 * S_CAST(uint64_t, value_ct);</span>
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7907
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7907" class="line" lang=""> } else if (value_type == 3) {</span>
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7908
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7908" class="line" lang=""> // int32, max len 11</span>
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7909
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7909" class="line" lang=""> cur_info_slen_ubound += 12 * S_CAST(uint64_t, value_ct);</span>
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7910
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7910" class="line" lang=""> } else if (value_type == 5) {</span>
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7911
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7911" class="line" lang=""> cur_info_slen_ubound += (kMaxFloatGSlen + 1) * S_CAST(uint64_t, value_ct);</span>
</pre>
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7912
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<td class="new_line diff-line-num old" data-linenumber="7892" style="width: 35px; color: rgba(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="LC7912" class="line" lang=""> } else {</span>
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7913
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<pre style="margin: 0;">-<span id="LC7913" class="line" lang=""> // string</span>
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7914
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<pre style="margin: 0;">-<span id="LC7914" class="line" lang=""> cur_info_slen_ubound += value_ct + 1;</span>
</pre>
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7892
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<pre style="margin: 0;">+<span id="LC7892" class="line" lang=""> const uint32_t key_slen = fif_slens[sidx];</span>
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7893
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<pre style="margin: 0;">+<span id="LC7893" class="line" lang=""> if (unlikely((!key_slen) || ScanBcfType(&parse_iter, &value_type, &value_ct) || (parse_iter > shared_end))) {</span>
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7894
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<pre style="margin: 0;">+<span id="LC7894" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
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7915
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7895
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<pre style="margin: 0;"> <span id="LC7895" class="line" lang=""> }</span>
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7916
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<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7916" class="line" lang=""> parse_iter = &(parse_iter[vec_byte_ct]);</span>
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7917
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<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7917" class="line" lang=""> } else {</span>
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7918
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<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7918" class="line" lang=""> // tolerate value_type == value_ct == 0 "untyped-missing" special</span>
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7919
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<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7919" class="line" lang=""> // case, but only if field is of type Flag. Note that this means the</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7920
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<pre style="margin: 0;">-<span id="LC7920" class="line" lang=""> // flag IS present (and yes, bcftools emits this since it's compact).</span>
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7921
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<pre style="margin: 0;">-<span id="LC7921" class="line" lang=""> //</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7922
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<pre style="margin: 0;">-<span id="LC7922" class="line" lang=""> // value_ct == 0, value_type == 7 is also valid (string, missing).</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7923
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<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7923" class="line" lang=""> //</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7924
</td>
<td class="new_line diff-line-num old" data-linenumber="7896" style="width: 35px; color: rgba(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="LC7924" class="line" lang=""> // Otherwise, value_ct == 0 should not happen.</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7925
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<pre style="margin: 0;">-<span id="LC7925" class="line" lang=""> if (!IsSet(info_flags, sidx)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7926
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<pre style="margin: 0;">-<span id="LC7926" class="line" lang=""> if (unlikely(value_ct != 7)) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7927" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7896
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<pre style="margin: 0;">+<span id="LC7896" class="line" lang=""> cur_info_slen_ubound += key_slen;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7927" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7897
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<pre style="margin: 0;">+<span id="LC7897" class="line" lang=""> if (value_ct) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7927" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7898
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<pre style="margin: 0;">+<span id="LC7898" class="line" lang=""> const uint32_t bytes_per_elem = kBcfBytesPerElem[value_type];</span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="7899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7899
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<pre style="margin: 0;">+<span id="LC7899" class="line" lang=""> const uint64_t vec_byte_ct = bytes_per_elem * S_CAST(uint64_t, value_ct);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7927" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7900
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<pre style="margin: 0;">+<span id="LC7900" class="line" lang=""> if (unlikely((!bytes_per_elem) || (S_CAST(uint64_t, shared_end - parse_iter) < vec_byte_ct))) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7927
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<td class="new_line diff-line-num" data-linenumber="7901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7901
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7901" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7928
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<td class="new_line diff-line-num" data-linenumber="7902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7902
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7902" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7929
</td>
<td class="new_line diff-line-num old" data-linenumber="7903" style="width: 35px; color: rgba(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>
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<pre style="margin: 0;">-<span id="LC7929" class="line" lang=""> cur_info_slen_ubound += 2;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7903
</td>
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<pre style="margin: 0;">+<span id="LC7903" class="line" lang=""> if (value_type == 1) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7904
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7904" class="line" lang=""> // int8, max len 4 ("-127"), add 1 for comma</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7905
</td>
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<pre style="margin: 0;">+<span id="LC7905" class="line" lang=""> cur_info_slen_ubound += 5 * S_CAST(uint64_t, value_ct);</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7906
</td>
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<pre style="margin: 0;">+<span id="LC7906" class="line" lang=""> } else if (value_type == 2) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7907
</td>
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<pre style="margin: 0;">+<span id="LC7907" class="line" lang=""> // int16, max len 6</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7908
</td>
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<pre style="margin: 0;">+<span id="LC7908" class="line" lang=""> cur_info_slen_ubound += 7 * S_CAST(uint64_t, value_ct);</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7909
</td>
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<pre style="margin: 0;">+<span id="LC7909" class="line" lang=""> } else if (value_type == 3) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7910
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7910" class="line" lang=""> // int32, max len 11</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7911
</td>
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<pre style="margin: 0;">+<span id="LC7911" class="line" lang=""> cur_info_slen_ubound += 12 * S_CAST(uint64_t, value_ct);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7912
</td>
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<pre style="margin: 0;">+<span id="LC7912" class="line" lang=""> } else if (value_type == 5) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7913
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7913" class="line" lang=""> cur_info_slen_ubound += (kMaxFloatGSlen + 1) * S_CAST(uint64_t, value_ct);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7914
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7914" class="line" lang=""> } else {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7915
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7915" class="line" lang=""> // string</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7916
</td>
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<pre style="margin: 0;">+<span id="LC7916" class="line" lang=""> cur_info_slen_ubound += value_ct + 1;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7917
</td>
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<pre style="margin: 0;">+<span id="LC7917" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7918
</td>
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<pre style="margin: 0;">+<span id="LC7918" class="line" lang=""> parse_iter = &(parse_iter[vec_byte_ct]);</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7919
</td>
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<pre style="margin: 0;">+<span id="LC7919" class="line" lang=""> } else {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7920
</td>
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<pre style="margin: 0;">+<span id="LC7920" class="line" lang=""> // tolerate value_type == value_ct == 0 "untyped-missing" special</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="7921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7921
</td>
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<pre style="margin: 0;">+<span id="LC7921" class="line" lang=""> // case, but only if field is of type Flag. Note that this means the</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7922
</td>
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<pre style="margin: 0;">+<span id="LC7922" class="line" lang=""> // flag IS present (and yes, bcftools emits this since it's compact).</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7923
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<pre style="margin: 0;">+<span id="LC7923" class="line" lang=""> //</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7924
</td>
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<pre style="margin: 0;">+<span id="LC7924" class="line" lang=""> // value_ct == 0, value_type == 7 is also valid (string, missing).</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7925
</td>
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<pre style="margin: 0;">+<span id="LC7925" class="line" lang=""> //</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7926
</td>
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<pre style="margin: 0;">+<span id="LC7926" class="line" lang=""> // Otherwise, value_ct == 0 should not happen.</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7927
</td>
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<pre style="margin: 0;">+<span id="LC7927" class="line" lang=""> if (!IsSet(info_flags, sidx)) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7928
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7928" class="line" lang=""> if (unlikely(value_ct != 7)) {</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7929
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<pre style="margin: 0;">+<span id="LC7929" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7930
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<pre style="margin: 0;">+<span id="LC7930" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7931
</td>
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<pre style="margin: 0;">+<span id="LC7931" class="line" lang=""> cur_info_slen_ubound += 2;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="7930" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7932
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7932" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="7930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7930
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<td class="new_line diff-line-num" data-linenumber="7933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7933
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7933" class="line" lang=""> }</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7931
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<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7931" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7932
</td>
<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7932" class="line" lang=""> if (sidx == pr_sidx) {</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7933
</td>
<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7933" class="line" lang=""> if (unlikely(info_pr_here)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7934
</td>
<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7934" class="line" lang=""> putc_unlocked('\n', stdout);</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7935
</td>
<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7935" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Variant record #%" PRIuPTR " in --bcf file has multiple INFO/PR entries.\n", vrec_idx);</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7936
</td>
<td class="new_line diff-line-num old" data-linenumber="7934" style="width: 35px; color: rgba(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="LC7936" class="line" lang=""> goto BcfToPgen_ret_MALFORMED_INPUT_WW;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7934
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7934" class="line" lang=""> if (sidx == pr_sidx) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7935
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7935" class="line" lang=""> if (unlikely(info_pr_here)) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7936
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7936" class="line" lang=""> putc_unlocked('\n', stdout);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7937
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7937" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Variant record #%" PRIuPTR " in --bcf file has multiple INFO/PR entries.\n", vrec_idx);</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7938
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7938" class="line" lang=""> goto BcfToPgen_ret_MALFORMED_INPUT_WW;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="7939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7939
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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="LC7939" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="7937" style="width: 35px; color: rgba(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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7940
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<pre style="margin: 0;">+<span id="LC7940" class="line" lang=""> info_pr_here = 1;</span>
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7937
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7941
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<pre style="margin: 0;"> <span id="LC7941" class="line" lang=""> }</span>
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7938
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<pre style="margin: 0;">-<span id="LC7938" class="line" lang=""> info_pr_here = 1;</span>
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7939
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7942
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<pre style="margin: 0;"> <span id="LC7942" class="line" lang=""> }</span>
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7940
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<td class="new_line diff-line-num old" data-linenumber="7943" style="width: 35px; color: rgba(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="LC7940" class="line" lang=""> <span class="idiff left right">}</span></span>
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7941
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<td class="new_line diff-line-num old" data-linenumber="7943" style="width: 35px; color: rgba(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="LC7941" class="line" lang=""> <span class="idiff left">if (cu</span>r_info_slen_ubound <span class="idiff">> filte</span>r_info_slen_ubound<span class="idiff right">) {</span></span>
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7942
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<td class="new_line diff-line-num old" data-linenumber="7943" style="width: 35px; color: rgba(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="LC7942" class="line" lang=""> <span class="idiff left right">filter_info_slen_ubound = cur_info_slen_ubound;</span></span>
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7943
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<pre style="margin: 0;">+<span id="LC7943" class="line" lang=""> <span class="idiff left right"> if (cur_info_slen_ubound > filter_info_slen_ubound) {</span></span>
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7944
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<pre style="margin: 0;">+<span id="LC7944" class="line" lang=""> <span class="idiff left"> filte</span>r_info_slen_ubound <span class="idiff">= cu</span>r_info_slen_ubound<span class="idiff right">;</span></span>
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7945
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<pre style="margin: 0;">+<span id="LC7945" class="line" lang=""> <span class="idiff left right">}</span></span>
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7943
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7946
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<pre style="margin: 0;"> <span id="LC7946" class="line" lang=""> }</span>
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7944
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7947
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<pre style="margin: 0;"> <span id="LC7947" class="line" lang=""> if (unlikely(parse_iter != shared_end)) {</span>
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7945
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<td class="new_line diff-line-num" data-linenumber="7948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7948
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<pre style="margin: 0;"> <span id="LC7948" class="line" lang=""> goto BcfToPgen_ret_VREC_GENERIC;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9199" style="width: 35px; color: rgba(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="9202" style="width: 35px; color: rgba(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">@@ -9199,7 +9202,7 @@ PglErr OxSampleToPsam(const char* samplename, const char* const_fid, const char*</td>
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<td class="old_line diff-line-num" data-linenumber="9199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9199
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<td class="new_line diff-line-num" data-linenumber="9202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9202
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<pre style="margin: 0;"> <span id="LC9202" class="line" lang=""> } else if (col_type_char == 'B') {</span>
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<td class="old_line diff-line-num" data-linenumber="9200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9200
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<td class="new_line diff-line-num" data-linenumber="9203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9203
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<pre style="margin: 0;"> <span id="LC9203" class="line" lang=""> at_least_one_binary_pheno = 1;</span>
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<td class="old_line diff-line-num" data-linenumber="9201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9201
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<td class="new_line diff-line-num" data-linenumber="9204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9204
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<pre style="margin: 0;"> <span id="LC9204" class="line" lang=""> cur_col_type = kOxSampleColBinary;</span>
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9202
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<td class="new_line diff-line-num old" data-linenumber="9205" style="width: 35px; color: rgba(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="LC9202" class="line" lang=""> } else if (col_type_char == 'P') {</span>
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9205
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<pre style="margin: 0;">+<span id="LC9205" class="line" lang=""> } else if <span class="idiff left">((col_type_char == 'C') || </span>(col_type_char == 'P')<span class="idiff right">)</span> {</span>
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9203
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<td class="new_line diff-line-num" data-linenumber="9206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9206
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<pre style="margin: 0;"> <span id="LC9206" class="line" lang=""> cur_col_type = kOxSampleColQuantitative;</span>
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9204
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<td class="new_line diff-line-num" data-linenumber="9207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9207
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<pre style="margin: 0;"> <span id="LC9207" class="line" lang=""> } else if (likely(col_type_char == '0')) {</span>
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9205
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<td class="new_line diff-line-num" data-linenumber="9208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9208
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<pre style="margin: 0;"> <span id="LC9208" class="line" lang=""> ++initial_skip_col_ct;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9888" style="width: 35px; color: rgba(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="9891" style="width: 35px; color: rgba(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">@@ -9888,13 +9891,40 @@ PglErr OxGenToPgen(const char* genname, const char* samplename, const char* cons</td>
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9888
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9891
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<pre style="margin: 0;"> <span id="LC9891" class="line" lang=""> uintptr_t variant_skip_ct = 0;</span>
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9889
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9892
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<pre style="margin: 0;"> <span id="LC9892" class="line" lang=""> char* line_iter = TextLineEnd(&gen_txs);</span>
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9890
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9893
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9893" class="line" lang=""> ++line_idx;</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9894
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9894" class="line" lang=""> if (unlikely(!TextGetUnsafe2(&gen_txs, &line_iter))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9895
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9895" class="line" lang=""> if (TextStreamErrcode2(&gen_txs, &reterr)) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9896
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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="LC9896" class="line" lang=""> goto OxGenToPgen_ret_TSTREAM_FAIL;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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">
9897
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9897" class="line" lang=""> }</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9898
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9898" class="line" lang=""> logerrputs("Error: Empty .gen file.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9899
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9899" class="line" lang=""> goto OxGenToPgen_ret_INCONSISTENT_INPUT;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9900
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9900" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9901
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9901" class="line" lang=""> uint32_t is_v2 = 0;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9902
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9902" class="line" lang=""> {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9903
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9903" class="line" lang=""> const uint32_t token_ct = CountTokens(line_iter);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9904
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9904" class="line" lang=""> const uint32_t expected_v2_token_ct = 3 * sample_ct + 6;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9905" class="line" lang=""> if (token_ct == expected_v2_token_ct) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9906" class="line" lang=""> is_v2 = 1;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9907
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9907" class="line" lang=""> } else if (unlikely(token_ct != expected_v2_token_ct - 1)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9908" class="line" lang=""> logerrprintfww("Error: Unexpected number of columns in .gen file (%u or %u expected).\n", expected_v2_token_ct - 1, expected_v2_token_ct);</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9909" class="line" lang=""> goto OxGenToPgen_ret_INCONSISTENT_INPUT;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9910" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9911" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9891" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9912" class="line" lang=""> goto OxGenToPgen_loop_start;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9891
</td>
<td class="new_line diff-line-num" data-linenumber="9913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9913
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9913" class="line" lang=""> for (; TextGetUnsafe2(&gen_txs, &line_iter); ++line_idx) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9892" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9914" class="line" lang=""> OxGenToPgen_loop_start:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9892" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9915" class="line" lang=""> ; // make this work with plain C, as opposed to just C++, compilers</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9892
</td>
<td class="new_line diff-line-num" data-linenumber="9916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9916
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9916" class="line" lang=""> char* chr_code_str = line_iter;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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">
9893
</td>
<td class="new_line diff-line-num" data-linenumber="9917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9917
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9917" class="line" lang=""> char* chr_code_end = CurTokenEnd(chr_code_str);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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
</td>
<td class="new_line diff-line-num" data-linenumber="9918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9918
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9918" class="line" lang=""> const char* variant_id_str = FirstNonTspace(chr_code_end);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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
</td>
<td class="new_line diff-line-num" 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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9919" class="line" lang=""> if (unlikely(IsEolnKns(*variant_id_str))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9896
</td>
<td class="new_line diff-line-num" 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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9920" class="line" lang=""> goto OxGenToPgen_ret_MISSING_TOKENS;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9897
</td>
<td class="new_line diff-line-num" 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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9921" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9922
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9922" class="line" lang=""> if (is_v2) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9923
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9923" class="line" lang=""> variant_id_str = FirstNonTspace(CurTokenEnd(variant_id_str));</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9924
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9924" class="line" lang=""> if (unlikely(IsEolnKns(*variant_id_str))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9925
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9925" class="line" lang=""> goto OxGenToPgen_ret_MISSING_TOKENS;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9926
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9926" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="9898" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="9927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9927
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9927" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9898
</td>
<td class="new_line diff-line-num" 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">
9928
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9928" class="line" lang=""></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9899
</td>
<td class="new_line diff-line-num" 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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9929" class="line" lang=""> if (!single_chr_str) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="9900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9900
</td>
<td class="new_line diff-line-num" 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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9930" class="line" lang=""> uint32_t cur_chr_code;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10055" style="width: 35px; color: rgba(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="10085" style="width: 35px; color: rgba(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">@@ -10055,10 +10085,6 @@ PglErr OxGenToPgen(const char* genname, const char* samplename, const char* cons</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10055
</td>
<td class="new_line diff-line-num" data-linenumber="10085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10085
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10085" class="line" lang=""> goto OxGenToPgen_ret_WRITE_FAIL;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10056
</td>
<td class="new_line diff-line-num" data-linenumber="10086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10086
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10086" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10057
</td>
<td class="new_line diff-line-num" data-linenumber="10087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10087
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10087" class="line" lang=""> if (unlikely(!variant_ct)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10058
</td>
<td class="new_line diff-line-num old" data-linenumber="10088" style="width: 35px; color: rgba(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="LC10058" class="line" lang=""> if (!variant_skip_ct) {</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10059
</td>
<td class="new_line diff-line-num old" data-linenumber="10088" style="width: 35px; color: rgba(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="LC10059" class="line" lang=""> logerrputs("Error: Empty .gen file.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10060
</td>
<td class="new_line diff-line-num old" data-linenumber="10088" style="width: 35px; color: rgba(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="LC10060" class="line" lang=""> goto OxGenToPgen_ret_INCONSISTENT_INPUT;</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10061
</td>
<td class="new_line diff-line-num old" data-linenumber="10088" style="width: 35px; color: rgba(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="LC10061" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10062
</td>
<td class="new_line diff-line-num" data-linenumber="10088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10088
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10088" class="line" lang=""> logerrprintfww("Error: All %" PRIuPTR " variant%s in .gen file skipped due to chromosome filter.\n", variant_skip_ct, (variant_skip_ct == 1)? "" : "s");</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10063
</td>
<td class="new_line diff-line-num" data-linenumber="10089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10089
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10089" class="line" lang=""> goto OxGenToPgen_ret_INCONSISTENT_INPUT;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10064
</td>
<td class="new_line diff-line-num" data-linenumber="10090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10090
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10090" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10138" style="width: 35px; color: rgba(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="10164" style="width: 35px; color: rgba(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">@@ -10138,7 +10164,7 @@ PglErr OxGenToPgen(const char* genname, const char* samplename, const char* cons</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10138
</td>
<td class="new_line diff-line-num" data-linenumber="10164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10164
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10164" class="line" lang=""> continue;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10139
</td>
<td class="new_line diff-line-num" data-linenumber="10165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10165
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10165" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="10140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10140
</td>
<td class="new_line diff-line-num" data-linenumber="10166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10166
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<pre style="margin: 0;"> <span id="LC10166" class="line" lang=""> }</span>
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10141
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<pre style="margin: 0;">-<span id="LC10141" class="line" lang=""> const char* linebuf_iter = NextTokenMult(FirstNonTspace(&(chr_code_end[1])), 4);</span>
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10167
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<pre style="margin: 0;">+<span id="LC10167" class="line" lang=""> const char* linebuf_iter = NextTokenMult(FirstNonTspace(&(chr_code_end[1])), 4<span class="idiff left right"> + is_v2</span>);</span>
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10142
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10168
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<pre style="margin: 0;"> <span id="LC10168" class="line" lang=""> uint32_t inner_loop_last = kBitsPerWordD2 - 1;</span>
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10143
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10169
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<pre style="margin: 0;"> <span id="LC10169" class="line" lang=""> Dosage* dosage_main_iter = dosage_main;</span>
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10144
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10170
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<pre style="margin: 0;"> <span id="LC10170" class="line" lang=""> for (uint32_t widx = 0; ; ++widx) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13843" style="width: 35px; color: rgba(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="13869" style="width: 35px; color: rgba(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">@@ -13843,6 +13869,14 @@ PglErr OxHapslegendToPgen(const char* hapsname, const char* legendname, const ch</td>
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13843
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13869
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<pre style="margin: 0;"> <span id="LC13869" class="line" lang=""> }</span>
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13844
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13870
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<pre style="margin: 0;"> <span id="LC13870" class="line" lang=""> reterr = InitTextStream(hapsname, max_line_blen, ClipU32(max_thread_ct - 1, 1, 4), &haps_txs);</span>
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13845
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13871
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<pre style="margin: 0;"> <span id="LC13871" class="line" lang=""> if (unlikely(reterr)) {</span>
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13872
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<pre style="margin: 0;">+<span id="LC13872" class="line" lang=""> if (reterr == kPglRetOpenFail) {</span>
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13873
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<pre style="margin: 0;">+<span id="LC13873" class="line" lang=""> const uint32_t slen = strlen(hapsname);</span>
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13874
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<pre style="margin: 0;">+<span id="LC13874" class="line" lang=""> if ((!StrEndsWith(hapsname, ".haps", slen)) &&</span>
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13875
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<pre style="margin: 0;">+<span id="LC13875" class="line" lang=""> (!StrEndsWith(hapsname, ".haps.gz", slen))) {</span>
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13876
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<pre style="margin: 0;">+<span id="LC13876" class="line" lang=""> logerrprintfww("Error: Failed to open %s : %s. (--haps expects a complete filename; did you forget '.haps' at the end?)\n", hapsname, strerror(errno));</span>
</pre>
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13877
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<pre style="margin: 0;">+<span id="LC13877" class="line" lang=""> goto OxHapslegendToPgen_ret_1;</span>
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13878
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<pre style="margin: 0;">+<span id="LC13878" class="line" lang=""> }</span>
</pre>
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13879
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<pre style="margin: 0;">+<span id="LC13879" class="line" lang=""> }</span>
</pre>
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13846
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13880
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<pre style="margin: 0;"> <span id="LC13880" class="line" lang=""> goto OxHapslegendToPgen_ret_TSTREAM_FAIL_HAPS;</span>
</pre>
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13847
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13881
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<pre style="margin: 0;"> <span id="LC13881" class="line" lang=""> }</span>
</pre>
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13848
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13882
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<pre style="margin: 0;"> <span id="LC13882" class="line" lang=""> unsigned char* bigstack_mark2 = g_bigstack_base;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13926" style="width: 35px; color: rgba(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="13960" style="width: 35px; color: rgba(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">@@ -13926,7 +13960,14 @@ PglErr OxHapslegendToPgen(const char* hapsname, const char* legendname, const ch</td>
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<td class="old_line diff-line-num" data-linenumber="13926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13926
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13960
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<pre style="margin: 0;"> <span id="LC13960" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13927
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<td class="new_line diff-line-num" data-linenumber="13961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13961
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13961" class="line" lang=""> reterr = InitTextStream(legendname, max_line_blen, 1, &legend_txs);</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13928
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<td class="new_line diff-line-num" data-linenumber="13962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13962
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<pre style="margin: 0;"> <span id="LC13962" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="13929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13929
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<td class="new_line diff-line-num old" data-linenumber="13963" style="width: 35px; color: rgba(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="LC13929" class="line" lang=""> goto OxHapslegendToPgen_ret_1;</span>
</pre>
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13963
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<pre style="margin: 0;">+<span id="LC13963" class="line" lang=""> if (reterr == kPglRetOpenFail) {</span>
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<td class="new_line diff-line-num new" data-linenumber="13964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13964
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<pre style="margin: 0;">+<span id="LC13964" class="line" lang=""> const uint32_t slen = strlen(legendname);</span>
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13965
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<pre style="margin: 0;">+<span id="LC13965" class="line" lang=""> if (!StrEndsWith(legendname, ".legend", slen)) {</span>
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13966
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<pre style="margin: 0;">+<span id="LC13966" class="line" lang=""> logerrprintfww("Error: Failed to open %s : %s. (--legend expects a complete filename; did you forget '.legend' at the end?)\n", legendname, strerror(errno));</span>
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13967
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<pre style="margin: 0;">+<span id="LC13967" class="line" lang=""> goto OxHapslegendToPgen_ret_1;</span>
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13968
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<pre style="margin: 0;">+<span id="LC13968" class="line" lang=""> }</span>
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13969
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<pre style="margin: 0;">+<span id="LC13969" class="line" lang=""> }</span>
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13970
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<pre style="margin: 0;">+<span id="LC13970" class="line" lang=""> goto OxHapslegendToPgen_ret_TSTREAM_FAIL_LEGEND;</span>
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13930
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13971
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<pre style="margin: 0;"> <span id="LC13971" class="line" lang=""> }</span>
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13931
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13972
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<pre style="margin: 0;"> <span id="LC13972" class="line" lang=""> ++line_idx_legend;</span>
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13932
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13973
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<pre style="margin: 0;"> <span id="LC13973" class="line" lang=""> char* legend_line_start = TextGet(&legend_txs);</span>
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<li id="77152f1b1412f42b6493e48b39abf3be847a626f">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#77152f1b1412f42b6493e48b39abf3be847a626f"><strong>plink2_merge.cc</strong></a>
The diff for this file was not included because it is too large.
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#59216b3409d1d2c9ff4b9a784709ac15d3a3e12c"><strong>plink2_merge.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">@@ -36,7 +36,8 @@ FLAGSET_DEF_START()</td>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergeSampleInnerJoin</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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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergeVariantInnerJoin</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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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergePhenoInnerJoin</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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39
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<td class="new_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergeMultiallelicsAlreadyJoined</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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergeMultiallelicsAlreadyJoined</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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPmergeOutputVzs</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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40
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">PmergeFlags</span><span class="p">);</span></span>
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41
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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42
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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">@@ -58,11 +59,12 @@ ENUM_U31_DEF_START()</td>
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58
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeXheaderMode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQicModeErase</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQicModeNmMatch</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQicModeNmFirst</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQicModeFirst</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeQicMode</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQualModeErase</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQualModeNmMatch</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQualModeNmFirst</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQualModeFirst</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeQualModeMin</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeQualMode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeFilterModeErase</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">@@ -72,6 +74,13 @@ ENUM_U31_DEF_START()</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeFilterModeNonpassUnion</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeFilterMode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeInfoCmModeErase</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeInfoCmModeNmMatch</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeInfoCmModeNmFirst</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeInfoCmModeFirst</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeInfoCmMode</span><span class="p">);</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="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">kSort0</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">kSortNone</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(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="117" style="width: 35px; color: rgba(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">@@ -108,10 +117,10 @@ typedef struct PmergeStruct {</td>
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108
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">MergePhenoMode</span> <span class="n" style="color: #333;">merge_sex_mode</span><span class="p">;</span></span>
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109
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">MergePhenoMode</span> <span class="n" style="color: #333;">merge_pheno_mode</span><span class="p">;</span></span>
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110
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeXheaderMode</span> <span class="n" style="color: #333;">merge_xheader_mode</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeQ<span class="idiff left right">ic</span>Mode</span> <span class="n" style="color: #333;">merge_qual_mode</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeQ<span class="idiff left right">ual</span>Mode</span> <span class="n" style="color: #333;">merge_qual_mode</span><span class="p">;</span></span>
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112
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeFilterMode</span> <span class="n" style="color: #333;">merge_filter_mode</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">Merge<span class="idiff left right">Qic</span>Mode</span> <span class="n" style="color: #333;">merge_info_mode</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">Merge<span class="idiff left right">Qic</span>Mode</span> <span class="n" style="color: #333;">merge_cm_mode</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">Merge<span class="idiff left right">InfoCm</span>Mode</span> <span class="n" style="color: #333;">merge_info_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">Merge<span class="idiff left right">InfoCm</span>Mode</span> <span class="n" style="color: #333;">merge_cm_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">merge_pheno_sort</span><span class="p">;</span></span>
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116
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">merge_info_sort</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_ct</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(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="128" style="width: 35px; color: rgba(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">@@ -119,6 +128,7 @@ typedef struct PmergeStruct {</td>
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128
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<pre style="margin: 0;"> <span id="LC128" 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_fname</span><span class="p">;</span></span>
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120
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129
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<pre style="margin: 0;"> <span id="LC129" 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;">psam_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC130" 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;">list_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC131" 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;">list_base_dir</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">PgenDiffStruct</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">@@ -138,7 +148,7 @@ void InitPgenDiff(PgenDiffInfo* pgen_diff_info_ptr);</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CleanupPgenDiff</span><span class="p">(</span><span class="n" style="color: #333;">PgenDiffInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgen_diff_info_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</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="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ImportFlags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">import_flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">sample_sort_mode</span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">missing_pheno</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;">SortMode</span> <span class="n" style="color: #333;">sort_vars_mode</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;">pgenname</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;">psamname</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;">pvarname</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="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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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</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="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">sample_sort_mode</span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">missing_pheno</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;">SortMode</span> <span class="n" style="color: #333;">sort_vars_mode</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;">pgenname</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;">psamname</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;">pvarname</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="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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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PgenDiff</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;">orig_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;">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="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;">PgenDiffInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pdip</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;">orig_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;">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;">max_allele_ct1</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_thread_ct</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1305,7 +1305,9 @@ PglErr Plink1ClusterImport(const char* within_fname, const char* catpheno_name,</td>
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1306" 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;">cat_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_iter</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="cpp"> <span class="n" style="color: #333;">cat_name_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;">cat_name_iter</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonnull_cat_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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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (5 May 2021): dropped this increment in mid-Jan refactor</span></span>
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nonnull_cat_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonnull_cat_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_names</span><span class="p">[</span><span class="n" style="color: #333;">cur_cat_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_start</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// permit duplicates if category is identical</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">@@ -6451,11 +6453,17 @@ PglErr SampleCounts(const uintptr_t* sample_include, const SampleIdInfo* siip, c</td>
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<pre style="margin: 0;"> <span id="LC6453" class="line" lang="cpp"> <span class="n" style="color: #333;">y_variant_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CountChrVariantsUnsafe</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;">y_code</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC6454" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC6455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">haploid_mask_lowbit</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;">haploid_mask</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">male_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC6455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">x_code</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6456" 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;">haploid_mask_lowbit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">XymtExists</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">kChrOffsetX</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6456" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (28 Mar 2021): if chrX is present, no autosomal diploid</span></span>
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<pre style="margin: 0;">+<span id="LC6457" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// chromosomes are present, and there are no males, we need to set the</span></span>
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<pre style="margin: 0;">+<span id="LC6458" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// low bit of chr_types and increment diploid_chr_type_ct.</span></span>
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<pre style="margin: 0;">+<span id="LC6459" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">x_code</span><span class="p">;</span></span>
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6460
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<pre style="margin: 0;">+<span id="LC6460" 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;">haploid_mask_lowbit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">XymtExists</span><span class="p">(</span><span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">kChrOffsetX</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x_code</span><span class="p">))</span> <span class="p">{</span></span>
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6461
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<pre style="margin: 0;">+<span id="LC6461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">male_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6457
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6462
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<pre style="margin: 0;"> <span id="LC6462" class="line" lang="cpp"> <span class="n" style="color: #333;">chr_types</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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6458
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6463
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<pre style="margin: 0;"> <span id="LC6463" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diploid_chr_type_ct</span><span class="p">;</span></span>
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6464
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<pre style="margin: 0;">+<span id="LC6464" 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><span class="n" style="color: #333;">chr_types</span><span class="p">)</span> <span class="p">{</span></span>
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6465
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<pre style="margin: 0;">+<span id="LC6465" class="line" lang="cpp"> <span class="n" style="color: #333;">chr_types</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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6466
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<pre style="margin: 0;">+<span id="LC6466" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">diploid_chr_type_ct</span><span class="p">;</span></span>
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6459
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6467
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<pre style="margin: 0;"> <span id="LC6467" class="line" lang="cpp"> <span class="p">}</span></span>
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6460
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6468
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<pre style="margin: 0;"> <span id="LC6468" class="line" lang="cpp"> <span class="p">}</span></span>
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6461
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6469
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<pre style="margin: 0;"> <span id="LC6469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y_variant_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" style="width: 35px; color: rgba(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="236" style="width: 35px; color: rgba(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">@@ -236,10 +236,6 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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236
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236
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<pre style="margin: 0;"> <span id="LC236" 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: IID column is not first or second in %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;">psamname</span><span class="p">);</span></span>
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237
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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238
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="p">}</span></span>
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239
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<pre style="margin: 0;">-<span id="LC239" 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;">psam_cols_mask</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;">col_types</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="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">col_skips</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="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" 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: SID column does not immediately follow IID column in %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;">psamname</span><span class="p">);</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="p">}</span></span>
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243
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239
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<pre style="margin: 0;"> <span id="LC239" 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;">in_interval</span><span class="p">))</span> <span class="p">{</span></span>
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244
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240
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<pre style="margin: 0;"> <span id="LC240" 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: --pheno-name range is inconsistent with %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;">psamname</span><span class="p">);</span></span>
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245
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_INCONSISTENT_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" style="width: 35px; color: rgba(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="244" style="width: 35px; color: rgba(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">@@ -248,6 +244,10 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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248
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">rpf_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">relevant_postfid_col_ct</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;">rpf_col_idx</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">rpf_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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249
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">rpf_col_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">rpf_col_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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250
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="p">}</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" 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;">psam_cols_mask</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;">col_types</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="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">col_skips</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="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" 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: SID column does not immediately follow IID column in %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;">psamname</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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251
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"></span>
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252
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<pre style="margin: 0;"> <span id="LC252" 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;">linebuf_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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253
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="787" style="width: 35px; color: rgba(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="787" style="width: 35px; color: rgba(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">@@ -787,9 +787,10 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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787
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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788
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">piip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sii</span><span class="p">.</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfSampleIdFidPresent</span><span class="p">;</span></span>
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789
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="p">}</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;">// special case: if there's exactly one phenotype and it's all-missing,</span></span>
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791
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// discard it</span></span>
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792
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pheno_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="p">(</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;">pheno_cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">nonmiss</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">)))</span> <span class="p">{</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;">// special case: if there's exactly one phenotype, it has the default name,</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;">// and it's all-missing, discard it. This removes forced .fam-derived and</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;">// similar phenotype columns, and is unlikely to break anything else.</span></span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pheno_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="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pheno_names_ptr</span><span class="p">,</span> <span class="s" style="color: #d14;">"PHENO1"</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;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">nonmiss</span><span class="p">,</span> <span class="n" style="color: #333;">raw_sample_ctl</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pheno_names_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pheno_names_ptr</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="LC796" class="line" lang="cpp"> <span class="n" style="color: #333;">CleanupPhenoCols</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_cols</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">@@ -450,7 +450,19 @@ void BackfillChrIdxs(const ChrInfo* cip, uint32_t chrs_encountered_m1, uint32_t</td>
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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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC453" 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;">PrInInfoToken</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</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="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PrInInfo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC454" 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;">info_token</span><span class="p">,</span> <span class="s" style="color: #d14;">"PR"</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="p">((</span><span class="n" style="color: #333;">info_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;">info_token</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="sc" style="color: #d14;">';'</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC455" 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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<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="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="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">info_token</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;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">info_slen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">]),</span> <span class="s" style="color: #d14;">";PR"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC458" 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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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">info_token</span><span class="p">[</span><span class="n" style="color: #333;">info_slen</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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<pre style="margin: 0;">+<span id="LC461" 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;">first_info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">info_token</span><span class="p">,</span> <span class="sc" style="color: #d14;">';'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">first_info_end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">strstr</span><span class="p">(</span><span class="n" style="color: #333;">info_token</span><span class="p">,</span> <span class="s" style="color: #d14;">";PR;"</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="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>
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<pre style="margin: 0;">+<span id="LC465" 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;">InfoPrStart</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</span><span class="p">)</span> <span class="p">{</span></span>
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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;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">info_token</span><span class="p">,</span> <span class="s" style="color: #d14;">"PR"</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="p">((</span><span class="n" style="color: #333;">info_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;">info_token</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="sc" style="color: #d14;">';'</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">info_token</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/cce84c08bbabda72d56f0ef78c4056523175bb52...d2773ed43c23f74d0db64432442fb669681849cf#60a6a1f914f822f6625c37a46f38a9ace19230bc"><strong>plink2_pvar.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">@@ -82,10 +82,12 @@ void VaridTemplateInit(const char* varid_template_str, const char* missing_id_ma</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC83" 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;">VaridTemplateWrite</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VaridTemplate</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vtp</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;">ref_start</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;">alt1_start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_bp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ref_token_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">extra_alt_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alt_token_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;">dst</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assume<span class="idiff left right">s</span> info_token[-1] is safe to read</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// may set info_token[info_slen] to \0, since <span class="idiff left">i</span>t need<span class="idiff right">s</span> to use strstr()</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">These functions </span>assume info_token[-1] is safe to read</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left">They </span>may set info_token[info_slen] to \0, since t<span class="idiff right">hey</span> need to use strstr()</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// (todo: try memmem()... except it isn't available on 32-bit mingw?)</span></span>
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<pre style="margin: 0;">-<span id="LC88" 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;">PrInInfoToken</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PrInInfo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC90" 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;">InfoPrStart</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_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;">info_token</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cip, max_variant_id_slen, and info_reload are in/out parameters.</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Chromosome filtering is performed if cip requests it.</span></span>
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