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<h3>
Michael R. Crusoe pushed to branch upstream
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/5e40e318e55cd4f81d08e4b2fbd288accd81b922">5e40e318</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-12-23T16:31:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-201212+dfsg</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
</a>
</li>
<li class="file-stats">
<a href="#5c0ac48ba397674ac28142efc3b29b7de442d076">
plink2_cmdline.cc
</a>
</li>
<li class="file-stats">
<a href="#353424a9b88ab7aad403c3734bdd60f28af6b661">
plink2_cmdline.h
</a>
</li>
<li class="file-stats">
<a href="#0bb44e45468b97ef0c21ed5ca6767a690fbf6626">
plink2_export.cc
</a>
</li>
<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
</a>
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<li class="file-stats">
<a href="#9e0620cca890479e38d176e292c73012d6b0f630">
plink2_matrix_calc.cc
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</ul>
<h4>Changes:</h4>
<li id="e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/5e40e318e55cd4f81d08e4b2fbd288accd81b922#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">@@ -70,7 +70,7 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="">#ifdef USE_MKL</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang=""> " Intel"</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="">#endif</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang=""> " (<span class="idiff left right">28 Oct</span> 2020)";</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang=""> " (<span class="idiff left right">12 Dec</span> 2020)";</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="">static const char ver_str2[] =</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> ""</span>
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<li id="5c0ac48ba397674ac28142efc3b29b7de442d076">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/5e40e318e55cd4f81d08e4b2fbd288accd81b922#5c0ac48ba397674ac28142efc3b29b7de442d076"><strong>plink2_cmdline.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); 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="710" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -710,6 +710,15 @@ BoolErr bigstack_calloc_u64(uintptr_t ct, uint64_t** u64_arr_ptr) {</td>
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710
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<pre style="margin: 0;"> <span id="LC710" 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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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_v</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="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">v_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v_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="n" style="color: #333;">VecW</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="n" style="color: #333;">kBytesPerVec</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" 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;">v_arr_ptr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" 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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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroVecArr</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;">v_arr_ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(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="LC719" 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="LC720" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_cp</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;">cp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cp_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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715
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724
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<pre style="margin: 0;"> <span id="LC724" 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;">cp_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="2005" style="width: 35px; color: rgba(0,0,0,0.3); 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="2014" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2005,6 +2014,24 @@ void CopyBitarrRange(const uintptr_t* __restrict src_bitarr, uintptr_t src_start</td>
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2005
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2014
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<pre style="margin: 0;"> <span id="LC2014" class="line" lang="cpp"> <span class="p">}</span></span>
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2006
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2015
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<pre style="margin: 0;"> <span id="LC2015" class="line" lang="cpp"><span class="p">}</span></span>
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2007
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2016
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<pre style="margin: 0;"> <span id="LC2016" class="line" lang="cpp"></span>
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2017
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<pre style="margin: 0;">+<span id="LC2017" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VerticalCounterUpdate</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;">acc1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">acc1_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="n" style="color: #333;">rem15_and_255d15</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc4_8_32</span><span class="p">)</span> <span class="p">{</span></span>
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2018
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<pre style="margin: 0;">+<span id="LC2018" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr1To4</span><span class="p">(</span><span class="n" style="color: #333;">acc1</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_8_32</span><span class="p">);</span></span>
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2019
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<pre style="margin: 0;">+<span id="LC2019" class="line" lang="cpp"> <span class="n" style="color: #333;">rem15_and_255d15</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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2020
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<pre style="margin: 0;">+<span id="LC2020" 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;">rem15_and_255d15</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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2021
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<pre style="margin: 0;">+<span id="LC2021" 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;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acc1_vec_ct</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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2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc8</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;">acc4_8_32</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">]);</span></span>
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2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr4To8</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_8_32</span><span class="p">,</span> <span class="n" style="color: #333;">acc8</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2024
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<pre style="margin: 0;">+<span id="LC2024" class="line" lang="cpp"> <span class="n" style="color: #333;">rem15_and_255d15</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;">15</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="cpp"> <span class="n" style="color: #333;">rem15_and_255d15</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>
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<td class="diff-line-num new new_line" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2026
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<pre style="margin: 0;">+<span id="LC2026" 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;">rem15_and_255d15</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2027
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<pre style="margin: 0;">+<span id="LC2027" 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;">acc8_vec_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acc4_vec_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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2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc32</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;">acc8</span><span class="p">[</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">]);</span></span>
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2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr8To32</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">acc8</span><span class="p">,</span> <span class="n" style="color: #333;">acc32</span><span class="p">);</span></span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="cpp"> <span class="n" style="color: #333;">rem15_and_255d15</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;">17</span><span class="p">;</span></span>
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2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="cpp"> <span class="p">}</span></span>
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2032
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<pre style="margin: 0;">+<span id="LC2032" class="line" lang="cpp"> <span class="p">}</span></span>
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2033
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="cpp"><span class="p">}</span></span>
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2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="cpp"></span>
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2008
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// advances forward_ct set bits; forward_ct must be positive. (stays put if</span></span>
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2009
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2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// forward_ct == 1 and current bit is set. may want to tweak this interface,</span></span>
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2010
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2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// easy to introduce off-by-one bugs...)</span></span>
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<li id="353424a9b88ab7aad403c3734bdd60f28af6b661">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/5e40e318e55cd4f81d08e4b2fbd288accd81b922#353424a9b88ab7aad403c3734bdd60f28af6b661"><strong>plink2_cmdline.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); 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="628" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -628,6 +628,8 @@ BoolErr bigstack_calloc_w(uintptr_t ct, uintptr_t** w_arr_ptr);</td>
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"></span>
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_u64</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;">uint64_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">u64_arr_ptr</span><span class="p">);</span></span>
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630
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_v</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="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">v_arr_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"></span>
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">bigstack_calloc_cp</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;">cp_arr_ptr</span><span class="p">);</span></span>
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632
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp"></span>
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635
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<pre style="margin: 0;"> <span id="LC635" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); 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="1654" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1652,6 +1654,8 @@ HEADER_INLINE void Vcount0Incr8To32(uint32_t acc8_vec_ct, VecW* acc8_iter, VecW*</td>
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1652
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="cpp"> <span class="p">}</span></span>
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1653
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="cpp"><span class="p">}</span></span>
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1654
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1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="cpp"></span>
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1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VerticalCounterUpdate</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;">acc1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">acc1_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="n" style="color: #333;">rem15_and_255d15</span><span class="p">,</span> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc4_8_32</span><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>
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="cpp"></span>
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1656
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// forward_ct must be positive. Stays put if forward_ct == 1 and current bit</span></span>
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1657
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is set.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9718" style="width: 35px; color: rgba(0,0,0,0.3); 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="9718" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9718,7 +9718,7 @@ PglErr Export012Smaj(const char* outname, const uintptr_t* orig_sample_include,</td>
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9718
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9718
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<pre style="margin: 0;"> <span id="LC9718" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (calc_thread_ct * kDosagePerCacheline * 2.375 + variant_ct * 2)</span></span>
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9719
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9719
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<pre style="margin: 0;"> <span id="LC9719" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">bytes_avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bigstack_left</span><span class="p">();</span></span>
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9720
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9720
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<pre style="margin: 0;"> <span id="LC9720" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// account for rounding</span></span>
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9721
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<pre style="margin: 0;">-<span id="LC9721" 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;">round_ceil</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kCacheline</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kDosagePerCacheline</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</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="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Dosage</span></span><span class="p"><span class="idiff right">)</span>));</span></span>
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9721
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<pre style="margin: 0;">+<span id="LC9721" 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;">round_ceil</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kCacheline</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">calc_thread_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kCacheline</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kDosagePerCacheline</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</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="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)));</span></span>
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9722
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9722
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<pre style="margin: 0;"> <span id="LC9722" 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;">bytes_avail</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">round_ceil</span><span class="p">))</span> <span class="p">{</span></span>
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9723
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9723
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<pre style="margin: 0;"> <span id="LC9723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Export012Smaj_ret_NOMEM</span><span class="p">;</span></span>
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9724
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9724
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<pre style="margin: 0;"> <span id="LC9724" 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">@@ -1370,9 +1370,10 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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1370
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="cpp"><span class="s" style="color: #d14;">" not suppressed.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1371
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1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="cpp"> <span class="p">);</span></span>
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1372
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"vcf</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">bcf</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">bgen</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">double-id</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">const-fid</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">id-delim</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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1373
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="cpp"><span class="s" style="color: #d14;">" --double-id : Set both FIDs and IIDs to the VCF/.bgen sample ID.</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="LC1374" class="line" lang="cpp"><span class="s" style="color: #d14;">" --const-fid [ID] : Set all FIDs to the given constant. If '0' (the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1375
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="cpp"><span class="s" style="color: #d14;">" default), no FID column is created.</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="LC1373" class="line" lang="cpp"><span class="s" style="color: #d14;">" --double-id : When importing single-part sample IDs, set both FID and</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"><span class="s" style="color: #d14;">" IID to the original ID.</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="LC1375" class="line" lang="cpp"><span class="s" style="color: #d14;">" --const-fid [ID] : When importing single-part sample IDs, set FID to the</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"><span class="s" style="color: #d14;">" given constant and IID to the original ID.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1376
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1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp"><span class="s" style="color: #d14;">" --id-delim [d] : Normally parses single-delimiter sample IDs as</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1377
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1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"><span class="s" style="color: #d14;">" <FID><d><IID>, and double-delimiter IDs as</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1378
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1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"><span class="s" style="color: #d14;">" <FID><d><IID><d><SID>; default delimiter is '_'.</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="5838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -5838,8 +5838,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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5838
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5838
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<pre style="margin: 0;"> <span id="LC5838" class="line" lang="cpp"> <span class="p">}</span></span>
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5839
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<pre style="margin: 0;"> <span id="LC5839" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># endif</span></span>
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5840
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5840
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<pre style="margin: 0;"> <span id="LC5840" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5841
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<pre style="margin: 0;">-<span id="LC5841" 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;">g_bigstack_base</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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5842
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<pre style="margin: 0;">-<span id="LC5842" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_end_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC5841" 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_end_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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5843
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5842
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<pre style="margin: 0;"> <span id="LC5842" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_end_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">qsr_include</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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5844
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5843
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<pre style="margin: 0;"> <span id="LC5843" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_end_alloc_cp</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">range_names</span><span class="p">)))</span> <span class="p">{</span></span>
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5845
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5844
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<pre style="margin: 0;"> <span id="LC5844" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ScoreReport_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5979" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5980,7 +5979,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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5980
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5979
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<pre style="margin: 0;"> <span id="LC5979" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ScoreReport_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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5981
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5980
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<pre style="margin: 0;"> <span id="LC5980" class="line" lang="cpp"> <span class="p">}</span></span>
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5982
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5981
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<pre style="margin: 0;"> <span id="LC5981" class="line" lang="cpp"> <span class="p">}</span></span>
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5983
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<pre style="margin: 0;">-<span id="LC5983" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">lines_to_skip_p1</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="p">((</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfScoreHeaderIgnore</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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5982
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<pre style="margin: 0;">+<span id="LC5982" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</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;">lines_to_skip_p1</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="p">((</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfScoreHeaderIgnore</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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5984
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5983
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<pre style="margin: 0;"> <span id="LC5983" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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5985
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5984
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<pre style="margin: 0;"> <span id="LC5984" 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;">lines_to_skip_p1</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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5986
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5985
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<pre style="margin: 0;"> <span id="LC5985" 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="6124" style="width: 35px; color: rgba(0,0,0,0.3); 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="6123" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6124,13 +6123,20 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6124
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6123
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<pre style="margin: 0;"> <span id="LC6123" class="line" lang="cpp"> <span class="n" style="color: #333;">raw_allele_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">[</span><span class="n" style="color: #333;">raw_variant_ct</span><span class="p">];</span></span>
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6125
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6124
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<pre style="margin: 0;"> <span id="LC6124" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6126
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6125
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<pre style="margin: 0;"> <span id="LC6125" 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;">raw_allele_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_allele_ct</span><span class="p">);</span></span>
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6126
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<pre style="margin: 0;">+<span id="LC6126" 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;">qsr_ct_nz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qsr_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">qsr_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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6127
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6127
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<pre style="margin: 0;"> <span id="LC6127" 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="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6128
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6128
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<pre style="margin: 0;"> <span id="LC6128" 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;">sex_nonmale_collapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6129
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6129
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<pre style="margin: 0;"> <span id="LC6129" 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;">genovec_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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6130
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6130
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<pre style="margin: 0;"> <span id="LC6130" 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;">dosage_present_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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6131
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6131
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<pre style="margin: 0;"> <span id="LC6131" 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;">dosage_main_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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6132
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<pre style="margin: 0;">-<span id="LC6132" 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;">missing_acc1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6133
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<td class="diff-line-num new_line old" data-linenumber="6132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6133" 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;">missing_male_acc1</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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6132
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<pre style="margin: 0;">+<span id="LC6132" 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;">missing_bitvec</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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6133
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<pre style="margin: 0;">+<span id="LC6133" 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;">missing_male_bitvec</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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6134
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<pre style="margin: 0;">+<span id="LC6134" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_accx</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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6135
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<pre style="margin: 0;">+<span id="LC6135" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_male_accx</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 new new_line" data-linenumber="6136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6136
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<pre style="margin: 0;">+<span id="LC6136" 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;">allele_ct_bases</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6137
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<pre style="margin: 0;">+<span id="LC6137" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">male_allele_ct_deltas</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6138
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<pre style="margin: 0;">+<span id="LC6138" 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;">variant_ct_rems</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6139
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<pre style="margin: 0;">+<span id="LC6139" 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;">variant_hap_ct_rems</span><span class="p">;</span></span>
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6134
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<td class="diff-line-num new_line" data-linenumber="6140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6140
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<pre style="margin: 0;"> <span id="LC6140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ddosage_sums</span><span class="p">;</span></span>
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6135
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6141
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<pre style="margin: 0;"> <span id="LC6141" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">;</span></span>
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6136
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<td class="diff-line-num new_line" data-linenumber="6142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6142
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<pre style="margin: 0;"> <span id="LC6142" 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;">already_seen_variants</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6141" style="width: 35px; color: rgba(0,0,0,0.3); 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="6147" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6141,15 +6147,20 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6141
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6147
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<pre style="margin: 0;"> <span id="LC6147" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_d</span><span class="p">(</span><span class="n" style="color: #333;">kScoreVariantBlockSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score_final_col_ct</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;">score_coefs_cmaj</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>
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6142
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6148
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<pre style="margin: 0;"> <span id="LC6148" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_d</span><span class="p">(</span><span class="n" style="color: #333;">kScoreVariantBlockSize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">score_final_col_ct</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;">score_coefs_cmaj</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>
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6143
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<td class="diff-line-num new_line" data-linenumber="6149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6149
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<pre style="margin: 0;"> <span id="LC6149" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_d</span><span class="p">(</span><span class="n" style="color: #333;">score_final_col_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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">final_scores_cmaj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6144
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<td class="diff-line-num new_line old" data-linenumber="6150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6144" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (4 Nov 2017): need raw_sample_ctl here, not sample_ctl</span></span>
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<td class="diff-line-num old_line" data-linenumber="6145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6145
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6150
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<pre style="margin: 0;"> <span id="LC6150" 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="n" style="color: #333;">sample_include_cumulative_popcounts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6146
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<td class="diff-line-num new_line" data-linenumber="6151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6151
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<pre style="margin: 0;"> <span id="LC6151" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6147
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6152
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<pre style="margin: 0;"> <span id="LC6152" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genovec_buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num old_line" data-linenumber="6148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6148
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<td class="diff-line-num new_line" data-linenumber="6153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6153
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<pre style="margin: 0;"> <span id="LC6153" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dosage_present_buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
</pre>
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6154
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<pre style="margin: 0;"> <span id="LC6154" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_dosage</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;">dosage_main_buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6150
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<pre style="margin: 0;">-<span id="LC6150" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="mi" style="color: #099;">45</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc1_vec_ct</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;">missing_acc1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6151
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<pre style="margin: 0;">-<span id="LC6151" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="mi" style="color: #099;">45</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc1_vec_ct</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;">missing_male_acc1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6152
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<pre style="margin: 0;">-<span id="LC6152" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_u64</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;">ddosage_sums</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6155
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<pre style="margin: 0;">+<span id="LC6155" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">acc1_vec_ct</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;">missing_bitvec</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6156
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<pre style="margin: 0;">+<span id="LC6156" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">acc1_vec_ct</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;">missing_male_bitvec</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6157
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<pre style="margin: 0;">+<span id="LC6157" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_v</span><span class="p">(</span><span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">missing_accx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6158
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<pre style="margin: 0;">+<span id="LC6158" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_v</span><span class="p">(</span><span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">missing_male_accx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6159
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<pre style="margin: 0;">+<span id="LC6159" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allele_ct_bases</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6160
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<pre style="margin: 0;">+<span id="LC6160" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_i32</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">male_allele_ct_deltas</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6161
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<pre style="margin: 0;">+<span id="LC6161" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct_nz</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variant_ct_rems</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6162
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<pre style="margin: 0;">+<span id="LC6162" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct_nz</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variant_hap_ct_rems</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6163
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<pre style="margin: 0;">+<span id="LC6163" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_u64</span><span class="p">(</span><span class="n" style="color: #333;">qsr_ct_nz</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;">ddosage_sums</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6153
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6164
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<pre style="margin: 0;"> <span id="LC6164" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_u64</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;">ddosage_incrs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6154
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6165
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<pre style="margin: 0;"> <span id="LC6165" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">already_seen_variants</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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6155
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6166
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<pre style="margin: 0;"> <span id="LC6166" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">raw_allele_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">already_seen_alleles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6169" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6158,18 +6169,12 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6158
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6169
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<pre style="margin: 0;"> <span id="LC6169" class="line" lang="cpp"> <span class="p">}</span></span>
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6159
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6170
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<pre style="margin: 0;"> <span id="LC6170" class="line" lang="cpp"> <span class="n" style="color: #333;">SetThreadFuncAndData</span><span class="p">(</span><span class="n" style="color: #333;">CalcScoreThread</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tg</span><span class="p">);</span></span>
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6160
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6171
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<pre style="margin: 0;"> <span id="LC6171" class="line" lang="cpp"></span>
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6161
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<pre style="margin: 0;">-<span id="LC6161" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc4</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;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">missing_acc1</span><span class="p">)[</span><span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">]);</span></span>
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6162
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6162" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc8</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;">missing_diploid_acc4</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">]);</span></span>
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6163
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6163" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc32</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;">missing_diploid_acc8</span><span class="p">[</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">]);</span></span>
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6164
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<pre style="margin: 0;">-<span id="LC6164" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc4</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;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">missing_male_acc1</span><span class="p">)[</span><span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">]);</span></span>
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6165
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<pre style="margin: 0;">-<span id="LC6165" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc8</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;">missing_haploid_acc4</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">]);</span></span>
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6166
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6166" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc32</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;">missing_haploid_acc8</span><span class="p">[</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">]);</span></span>
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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;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc4</span><span class="p">);</span></span>
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6168
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6168" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc8</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;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc32</span><span class="p">);</span></span>
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6170
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6170" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">);</span></span>
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6171
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6171" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">);</span></span>
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6172
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6172" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroVecArr</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc32</span><span class="p">);</span></span>
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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;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6173
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<pre style="margin: 0;">+<span id="LC6173" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_ct_rems</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;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6174
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<pre style="margin: 0;">+<span id="LC6174" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_ct_rems</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;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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="n" style="color: #333;">variant_hap_ct_rems</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;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6176
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<pre style="margin: 0;">+<span id="LC6176" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_hap_ct_rems</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;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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6177
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<pre style="margin: 0;">+<span id="LC6177" class="line" lang="cpp"> <span class="p">}</span></span>
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6173
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<td class="diff-line-num new_line" 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="n" style="color: #333;">FillCumulativePopcounts</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_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include_cumulative_popcounts</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" 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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6179
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<pre style="margin: 0;"> <span id="LC6179" class="line" lang="cpp"> <span class="n" style="color: #333;">CopyBitarrSubset</span><span class="p">(</span><span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">);</span></span>
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6175
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6180
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<pre style="margin: 0;"> <span id="LC6180" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignedBitarrInvert</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6211" style="width: 35px; color: rgba(0,0,0,0.3); 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="6216" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6211,12 +6216,6 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6211
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6216
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<pre style="margin: 0;"> <span id="LC6216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">geno_slope</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kRecipDosageMax</span><span class="p">;</span></span>
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6212
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6217
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<pre style="margin: 0;"> <span id="LC6217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">geno_intercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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6213
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6218
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<pre style="margin: 0;"> <span id="LC6218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cur_allele_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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6214
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<pre style="margin: 0;">-<span id="LC6214" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct_rem15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6215
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<pre style="margin: 0;">-<span id="LC6215" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct_rem255d15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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6216
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<pre style="margin: 0;">-<span id="LC6216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_hap_ct_rem15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6217
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<pre style="margin: 0;">-<span id="LC6217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_hap_ct_rem255d15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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6218
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<pre style="margin: 0;">-<span id="LC6218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_ct_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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6219
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<pre style="margin: 0;">-<span id="LC6219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">male_allele_ct_delta</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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6220
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6219
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<pre style="margin: 0;"> <span id="LC6219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">valid_variant_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6221
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6220
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<pre style="margin: 0;"> <span id="LC6220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_var_id_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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6222
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6221
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<pre style="margin: 0;"> <span id="LC6221" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">duplicated_var_id_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6325" style="width: 35px; color: rgba(0,0,0,0.3); 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="6324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6325,9 +6324,9 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6325
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6324
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<pre style="margin: 0;"> <span id="LC6324" class="line" lang="cpp"></span>
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6326
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6325
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<pre style="margin: 0;"> <span id="LC6325" 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_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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6327
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6326
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<pre style="margin: 0;"> <span id="LC6326" 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_buf</span><span class="p">);</span></span>
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6328
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<pre style="margin: 0;">-<span id="LC6328" class="line" lang="cpp"> <span class="n" style="color: #333;">GenoarrToMissingnessUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">genovec_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">acc1</span></span><span class="p">);</span></span>
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6327
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<pre style="margin: 0;">+<span id="LC6327" class="line" lang="cpp"> <span class="n" style="color: #333;">GenoarrToMissingnessUnsafe</span><span class="p">(</span><span class="n" style="color: #333;">genovec_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">bitvec</span></span><span class="p">);</span></span>
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6329
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6328
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<pre style="margin: 0;"> <span id="LC6328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dosage_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6330
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<pre style="margin: 0;">-<span id="LC6330" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmask</span><span class="p">(</span><span class="n" style="color: #333;">dosage_present_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">acc1</span></span><span class="p">);</span></span>
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6329
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<pre style="margin: 0;">+<span id="LC6329" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmask</span><span class="p">(</span><span class="n" style="color: #333;">dosage_present_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">bitvec</span></span><span class="p">);</span></span>
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6331
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<pre style="margin: 0;"> <span id="LC6330" class="line" lang="cpp"> <span class="p">}</span></span>
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6332
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6331
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<pre style="margin: 0;"> <span id="LC6331" class="line" lang="cpp"> <span class="n" style="color: #333;">FillCurDdosageInts</span><span class="p">(</span><span class="n" style="color: #333;">genovec_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_present_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_main_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">is_nonx_haploid</span><span class="p">,</span> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">);</span></span>
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6333
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6332
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<pre style="margin: 0;"> <span id="LC6332" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ploidy_d</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">@@ -6339,25 +6338,47 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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<pre style="margin: 0;"> <span id="LC6338" 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;">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;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_nonmale_collapsed_bits</span><span class="p">);</span></span>
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6339
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<pre style="margin: 0;"> <span id="LC6339" class="line" lang="cpp"> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</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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6341
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<pre style="margin: 0;"> <span id="LC6340" class="line" lang="cpp"> <span class="p">}</span></span>
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6342
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<pre style="margin: 0;">-<span id="LC6342" class="line" lang="cpp"> <span class="n" style="color: #333;">male_allele_ct_delta</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">is_new_variant</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC6343" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmask</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_acc1</span><span class="p">);</span></span>
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6344
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<pre style="margin: 0;">-<span id="LC6344" 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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6345
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<pre style="margin: 0;">-<span id="LC6345" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_base</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">is_new_variant</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC6341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_new_variant</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6342" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6343" class="line" lang="cpp"> <span class="n" style="color: #333;">male_allele_ct_deltas</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="LC6344" 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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6345
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<pre style="margin: 0;">+<span id="LC6345" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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6346
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<pre style="margin: 0;">+<span id="LC6346" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6347
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<pre style="margin: 0;">+<span id="LC6347" 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;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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6348
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<pre style="margin: 0;">+<span id="LC6348" class="line" lang="cpp"> <span class="n" style="color: #333;">male_allele_ct_deltas</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6349
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<pre style="margin: 0;">+<span id="LC6349" class="line" lang="cpp"> <span class="p">}</span></span>
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6350
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<pre style="margin: 0;">+<span id="LC6350" class="line" lang="cpp"> <span class="p">}</span></span>
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6351
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<pre style="margin: 0;">+<span id="LC6351" class="line" lang="cpp"> <span class="p">}</span></span>
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6352
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<pre style="margin: 0;">+<span id="LC6352" class="line" lang="cpp"> <span class="p">}</span></span>
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6353
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<pre style="margin: 0;">+<span id="LC6353" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmask</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_bitvec</span><span class="p">);</span></span>
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6354
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<pre style="margin: 0;">+<span id="LC6354" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_new_variant</span><span class="p">)</span> <span class="p">{</span></span>
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6355
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<pre style="margin: 0;">+<span id="LC6355" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6356
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<pre style="margin: 0;">+<span id="LC6356" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_bases</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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6357
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<pre style="margin: 0;">+<span id="LC6357" 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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6358
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<pre style="margin: 0;">+<span id="LC6358" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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6359
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<pre style="margin: 0;">+<span id="LC6359" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6360
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<pre style="margin: 0;">+<span id="LC6360" 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;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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6361
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<pre style="margin: 0;">+<span id="LC6361" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_bases</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6362
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<pre style="margin: 0;">+<span id="LC6362" class="line" lang="cpp"> <span class="p">}</span></span>
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6363
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<pre style="margin: 0;">+<span id="LC6363" class="line" lang="cpp"> <span class="p">}</span></span>
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6364
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<pre style="margin: 0;">+<span id="LC6364" class="line" lang="cpp"> <span class="p">}</span></span>
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6346
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6365
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<pre style="margin: 0;"> <span id="LC6365" class="line" lang="cpp"> <span class="p">}</span></span>
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6347
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6366
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<pre style="margin: 0;"> <span id="LC6366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_new_variant</span><span class="p">)</span> <span class="p">{</span></span>
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6348
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<pre style="margin: 0;">-<span id="LC6348" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr1To4</span><span class="p">(</span><span class="n" style="color: #333;">missing_acc1</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">);</span></span>
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6349
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<td class="diff-line-num new_line old" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6349" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_hap_ct_rem15</span><span class="p">))</span> <span class="p">{</span></span>
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6350
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<pre style="margin: 0;">-<span id="LC6350" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr4To8</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">);</span></span>
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6351
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<td class="diff-line-num new_line old" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6351" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_hap_ct_rem15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6352
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<td class="diff-line-num new_line old" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6352" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_hap_ct_rem255d15</span><span class="p">))</span> <span class="p">{</span></span>
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6353
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<pre style="margin: 0;">-<span id="LC6353" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr8To32</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc32</span><span class="p">);</span></span>
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6354
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<td class="diff-line-num new_line old" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6354" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_hap_ct_rem255d15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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6367
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<pre style="margin: 0;">+<span id="LC6367" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6368
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<pre style="margin: 0;">+<span id="LC6368" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">variant_hap_ct_rems</span><span class="p">,</span> <span class="n" style="color: #333;">missing_male_accx</span><span class="p">);</span></span>
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6369
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<pre style="margin: 0;">+<span id="LC6369" 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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6370
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<pre style="margin: 0;">+<span id="LC6370" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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6371
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<pre style="margin: 0;">+<span id="LC6371" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6372
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<pre style="margin: 0;">+<span id="LC6372" 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;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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6373
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<pre style="margin: 0;">+<span id="LC6373" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_bases</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6374
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<pre style="margin: 0;">+<span id="LC6374" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">variant_ct_rems</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;">qsr_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_accx</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_idx</span><span class="p">]));</span></span>
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6375
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<pre style="margin: 0;">+<span id="LC6375" class="line" lang="cpp"> <span class="p">}</span></span>
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6355
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6376
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<pre style="margin: 0;"> <span id="LC6376" class="line" lang="cpp"> <span class="p">}</span></span>
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6356
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6377
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<pre style="margin: 0;"> <span id="LC6377" class="line" lang="cpp"> <span class="p">}</span></span>
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6357
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6378
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<pre style="margin: 0;"> <span id="LC6378" class="line" lang="cpp"> <span class="p">}</span></span>
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6358
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6379
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<pre style="margin: 0;"> <span id="LC6379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_y</span><span class="p">)</span> <span class="p">{</span></span>
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6359
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<pre style="margin: 0;">-<span id="LC6359" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_acc1</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</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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6360
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<pre style="margin: 0;">-<span id="LC6360" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecOr</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">acc1</span></span><span class="p">);</span></span>
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6380
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<pre style="margin: 0;">+<span id="LC6380" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_bitvec</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</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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6381
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<pre style="margin: 0;">+<span id="LC6381" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecOr</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">bitvec</span></span><span class="p">);</span></span>
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6361
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6382
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<pre style="margin: 0;"> <span id="LC6382" class="line" lang="cpp"> <span class="p">}</span></span>
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6362
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6383
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<pre style="margin: 0;"> <span id="LC6383" class="line" lang="cpp"> <span class="n" style="color: #333;">ploidy_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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6363
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6384
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<pre style="margin: 0;"> <span id="LC6384" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6368" style="width: 35px; color: rgba(0,0,0,0.3); 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="6389" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6368,35 +6389,39 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6368
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6389
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<pre style="margin: 0;"> <span id="LC6389" 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;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter0</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_idx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_nonmale_collapsed_inv_bits</span><span class="p">);</span></span>
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6369
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6390
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<pre style="margin: 0;"> <span id="LC6390" class="line" lang="cpp"> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</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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6370
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6391
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<pre style="margin: 0;"> <span id="LC6391" class="line" lang="cpp"> <span class="p">}</span></span>
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6371
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<pre style="margin: 0;">-<span id="LC6371" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmaskCopy</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nonmale_collapsed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_male_acc1</span></span><span class="p">);</span></span>
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6372
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<pre style="margin: 0;">-<span id="LC6372" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAnd</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">acc1</span></span><span class="p">);</span></span>
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6392
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<pre style="margin: 0;">+<span id="LC6392" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecInvmaskCopy</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nonmale_collapsed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_male_bitvec</span></span><span class="p">);</span></span>
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6393
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<pre style="margin: 0;">+<span id="LC6393" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAnd</span><span class="p">(</span><span class="n" style="color: #333;">sex_nonmale_collapsed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">missing_<span class="idiff left right">bitvec</span></span><span class="p">);</span></span>
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6373
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6394
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<pre style="margin: 0;"> <span id="LC6394" class="line" lang="cpp"> <span class="p">}</span></span>
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6374
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6395
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<pre style="margin: 0;"> <span id="LC6395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_new_variant</span><span class="p">)</span> <span class="p">{</span></span>
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6375
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<pre style="margin: 0;">-<span id="LC6375" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr1To4</span><span class="p">(</span><span class="n" style="color: #333;">missing_acc1</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc4</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6376
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6376" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_ct_rem15</span><span class="p">))</span> <span class="p">{</span></span>
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6377
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6377" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr4To8</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">);</span></span>
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6378
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6378" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_ct_rem15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6379
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6379" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_ct_rem255d15</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6380
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6380" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr8To32</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc32</span><span class="p">);</span></span>
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6381
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<td class="diff-line-num new_line old" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6381" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_ct_rem255d15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6396
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<pre style="margin: 0;">+<span id="LC6396" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6397
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<pre style="margin: 0;">+<span id="LC6397" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_bases</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;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6398
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<pre style="margin: 0;">+<span id="LC6398" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct_rems</span><span class="p">,</span> <span class="n" style="color: #333;">missing_accx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6399
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<pre style="margin: 0;">+<span id="LC6399" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6400
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<pre style="margin: 0;">+<span id="LC6400" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6401
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<pre style="margin: 0;">+<span id="LC6401" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6402
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<pre style="margin: 0;">+<span id="LC6402" 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;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6403
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<pre style="margin: 0;">+<span id="LC6403" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_bases</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6404
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<pre style="margin: 0;">+<span id="LC6404" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">variant_ct_rems</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;">qsr_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">missing_accx</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_idx</span><span class="p">]));</span></span>
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6405
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<pre style="margin: 0;">+<span id="LC6405" class="line" lang="cpp"> <span class="p">}</span></span>
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6382
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6406
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<pre style="margin: 0;"> <span id="LC6406" class="line" lang="cpp"> <span class="p">}</span></span>
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6383
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6407
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<pre style="margin: 0;"> <span id="LC6407" class="line" lang="cpp"> <span class="p">}</span></span>
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6384
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<pre style="margin: 0;">-<span id="LC6384" class="line" lang="cpp"> <span class="n" style="color: #333;">allele_ct_base</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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6385
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6408
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<pre style="margin: 0;"> <span id="LC6408" class="line" lang="cpp"> <span class="p">}</span></span>
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6386
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6409
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<pre style="margin: 0;"> <span id="LC6409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_relevant_x</span><span class="p">)</span> <span class="p">{</span></span>
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6387
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6410
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<pre style="margin: 0;"> <span id="LC6410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_new_variant</span><span class="p">)</span> <span class="p">{</span></span>
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6388
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<pre style="margin: 0;">-<span id="LC6388" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">male_allele_ct_delta</span><span class="p">;</span></span>
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6389
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6389" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr1To4</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_acc1</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">);</span></span>
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6390
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6390" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_hap_ct_rem15</span><span class="p">))</span> <span class="p">{</span></span>
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6391
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6391" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr4To8</span><span class="p">(</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">);</span></span>
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6392
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6392" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_hap_ct_rem15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>
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6393
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6393" 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="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">variant_hap_ct_rem255d15</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6394
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<pre style="margin: 0;">-<span id="LC6394" class="line" lang="cpp"> <span class="n" style="color: #333;">Vcount0Incr8To32</span><span class="p">(</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc32</span><span class="p">);</span></span>
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6395
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<td class="diff-line-num new_line old" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6395" class="line" lang="cpp"> <span class="n" style="color: #333;">variant_hap_ct_rem255d15</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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6411
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<pre style="margin: 0;">+<span id="LC6411" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6412
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<pre style="margin: 0;">+<span id="LC6412" class="line" lang="cpp"> <span class="n" style="color: #333;">male_allele_ct_deltas</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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<td class="diff-line-num new new_line" data-linenumber="6413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6413
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<pre style="margin: 0;">+<span id="LC6413" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">variant_hap_ct_rems</span><span class="p">,</span> <span class="n" style="color: #333;">missing_male_accx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6414
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<pre style="margin: 0;">+<span id="LC6414" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6415
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<pre style="margin: 0;">+<span id="LC6415" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6416
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<pre style="margin: 0;">+<span id="LC6416" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6417
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<pre style="margin: 0;">+<span id="LC6417" 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;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6418
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<pre style="margin: 0;">+<span id="LC6418" class="line" lang="cpp"> <span class="n" style="color: #333;">male_allele_ct_deltas</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6419
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<pre style="margin: 0;">+<span id="LC6419" class="line" lang="cpp"> <span class="n" style="color: #333;">VerticalCounterUpdate</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_bitvec</span><span class="p">,</span> <span class="n" style="color: #333;">acc1_vec_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">variant_hap_ct_rems</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;">qsr_idx</span><span class="p">]),</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_accx</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_idx</span><span class="p">]));</span></span>
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6420
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<pre style="margin: 0;">+<span id="LC6420" class="line" lang="cpp"> <span class="p">}</span></span>
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6396
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6421
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<pre style="margin: 0;"> <span id="LC6421" class="line" lang="cpp"> <span class="p">}</span></span>
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6397
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6422
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<pre style="margin: 0;"> <span id="LC6422" class="line" lang="cpp"> <span class="p">}</span></span>
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6398
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6423
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<pre style="margin: 0;"> <span id="LC6423" class="line" lang="cpp"> <span class="p">}</span></span>
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6399
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<td class="diff-line-num new_line old" data-linenumber="6424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6399" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecOr</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_acc1</span></span><span class="p">);</span></span>
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6424
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<pre style="margin: 0;">+<span id="LC6424" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecOr</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_bitvec</span></span><span class="p">);</span></span>
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6400
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6425
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<pre style="margin: 0;"> <span id="LC6425" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6401
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6426
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<pre style="margin: 0;"> <span id="LC6426" 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;">domrec</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6402
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6427
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<pre style="margin: 0;"> <span id="LC6427" class="line" lang="cpp"> <span class="n" style="color: #333;">ploidy_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6421" style="width: 35px; color: rgba(0,0,0,0.3); 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="6446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6421,8 +6446,20 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6421
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6446
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<pre style="margin: 0;"> <span id="LC6446" class="line" lang="cpp"> <span class="n" style="color: #333;">ploidy_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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6422
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6447
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<pre style="margin: 0;"> <span id="LC6447" class="line" lang="cpp"> <span class="p">}</span></span>
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6423
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<td class="diff-line-num new_line" data-linenumber="6448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6448
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<pre style="margin: 0;"> <span id="LC6448" class="line" lang="cpp"> <span class="p">}</span></span>
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6424
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<td class="diff-line-num new_line old" data-linenumber="6449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6424" 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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6425
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<td class="diff-line-num new_line old" data-linenumber="6449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6425" class="line" lang="cpp"> <span class="n" style="color: #333;">ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6449
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<pre style="margin: 0;">+<span id="LC6449" 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;">qsr_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6450
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<pre style="margin: 0;">+<span id="LC6450" 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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6451
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<pre style="margin: 0;">+<span id="LC6451" class="line" lang="cpp"> <span class="n" style="color: #333;">ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">];</span></span>
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6452
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<pre style="margin: 0;">+<span id="LC6452" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6453
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<pre style="margin: 0;">+<span id="LC6453" 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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6454
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<pre style="margin: 0;">+<span id="LC6454" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6455
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<pre style="margin: 0;">+<span id="LC6455" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6456
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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="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">))</span> <span class="p">{</span></span>
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6457
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<pre style="margin: 0;">+<span id="LC6457" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_ddosage_sums</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;">ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">]);</span></span>
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6458
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<pre style="margin: 0;">+<span id="LC6458" 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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6459
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<pre style="margin: 0;">+<span id="LC6459" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</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="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="p">}</span></span>
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6462
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<pre style="margin: 0;">+<span id="LC6462" class="line" lang="cpp"> <span class="p">}</span></span>
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6426
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6463
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<pre style="margin: 0;"> <span id="LC6463" class="line" lang="cpp"> <span class="p">}</span></span>
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6427
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6464
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<pre style="margin: 0;"> <span id="LC6464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_freqs</span><span class="p">)</span> <span class="p">{</span></span>
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6428
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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;">cur_allele_freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetAlleleFreq</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">allele_freqs</span><span class="p">[</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="p">]),</span> <span class="n" style="color: #333;">cur_allele_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_allele_ct</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6449" style="width: 35px; color: rgba(0,0,0,0.3); 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="6486" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6449,7 +6486,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6449
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6486
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<pre style="margin: 0;"> <span id="LC6486" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// wraparound</span></span>
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6450
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6487
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<pre style="margin: 0;"> <span id="LC6487" class="line" lang="cpp"> <span class="n" style="color: #333;">geno_intercept</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">kDosageMax</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ploidy_d</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_allele_freq</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geno_slope</span><span class="p">;</span></span>
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6451
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6488
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<pre style="margin: 0;"> <span id="LC6488" class="line" lang="cpp"> <span class="p">}</span></span>
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6452
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<td class="diff-line-num new_line old" data-linenumber="6489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6452" 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;">missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left right">acc1</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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6489
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<pre style="margin: 0;">+<span id="LC6489" 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;">missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left right">bitvec</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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6453
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6490
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<pre style="margin: 0;"> <span id="LC6490" 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;">nm_sample_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">missing_ct</span><span class="p">;</span></span>
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6454
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6491
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<pre style="margin: 0;"> <span id="LC6491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">missing_ct</span><span class="p">)</span> <span class="p">{</span></span>
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6455
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6492
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<pre style="margin: 0;"> <span id="LC6492" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">missing_effect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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">@@ -6460,40 +6497,40 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6460
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6497
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<pre style="margin: 0;"> <span id="LC6497" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_y</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">is_relevant_x</span><span class="p">)</span> <span class="p">{</span></span>
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6461
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6498
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<pre style="margin: 0;"> <span id="LC6498" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroDArr</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">cur_dosages_vmaj_iter</span><span class="p">);</span></span>
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6462
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6499
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<pre style="margin: 0;"> <span id="LC6499" 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;">no_meanimpute</span><span class="p">)</span> <span class="p">{</span></span>
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6463
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<pre style="margin: 0;">-<span id="LC6463" 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;">male_missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left right">acc1</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</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="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_male_<span class="idiff left">acc1_bits</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">missing_male_acc1</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6500
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<pre style="margin: 0;">+<span id="LC6500" 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;">male_missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left right">bitvec</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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6501
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<pre style="margin: 0;">+<span id="LC6501" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_male_<span class="idiff left">bits</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">missing_male_bitvec</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6465
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6502
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<pre style="margin: 0;"> <span id="LC6502" 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;">male_missing_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;">male_missing_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">male_missing_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">male_missing_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6466
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<td class="diff-line-num new_line old" data-linenumber="6503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6466" 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;">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;">missing_male_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_male_acc1</span>_bits</span><span class="p">);</span></span>
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6503
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<pre style="margin: 0;">+<span id="LC6503" 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;">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;">missing_male_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_male</span>_bits</span><span class="p">);</span></span>
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6467
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6504
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<pre style="margin: 0;"> <span id="LC6504" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_dosages_vmaj_iter</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing_effect</span><span class="p">;</span></span>
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6468
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6505
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<pre style="margin: 0;"> <span id="LC6505" class="line" lang="cpp"> <span class="p">}</span></span>
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6469
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6506
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<pre style="margin: 0;"> <span id="LC6506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_relevant_x</span><span class="p">)</span> <span class="p">{</span></span>
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6470
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<pre style="margin: 0;">-<span id="LC6470" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// missing_male_<span class="idiff left right">acc1</span> not used after this point, so okay to</span></span>
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6507
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<pre style="margin: 0;">+<span id="LC6507" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// missing_male_<span class="idiff left right">bitvec</span> not used after this point, so okay to</span></span>
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6471
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6508
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<pre style="margin: 0;"> <span id="LC6508" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use buffer for nonmales</span></span>
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6472
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<pre style="margin: 0;">-<span id="LC6472" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAndCopy</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nonmale_collapsed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_male_acc1</span></span><span class="p">);</span></span>
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6509
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<pre style="margin: 0;">+<span id="LC6509" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAndCopy</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nonmale_collapsed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_ctl</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_male_bitvec</span></span><span class="p">);</span></span>
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6473
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6510
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<pre style="margin: 0;"> <span id="LC6510" class="line" lang="cpp"> <span class="n" style="color: #333;">missing_effect</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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6474
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6511
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<pre style="margin: 0;"> <span id="LC6511" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (8 Jul 2018): need to reset sample_idx</span></span>
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6475
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6512
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<pre style="margin: 0;"> <span id="LC6512" class="line" lang="cpp"> <span class="n" style="color: #333;">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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6476
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<pre style="margin: 0;">-<span id="LC6476" class="line" lang="cpp"> <span class="n" style="color: #333;">missing_male_<span class="idiff left">acc1_bits</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">missing_male_acc1</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6477
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<td class="diff-line-num new_line old" data-linenumber="6513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6477" 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;">nonmale_missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left right">acc1</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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6513
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<pre style="margin: 0;">+<span id="LC6513" class="line" lang="cpp"> <span class="n" style="color: #333;">missing_male_<span class="idiff left">bits</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">missing_male_bitvec</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6514
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<pre style="margin: 0;">+<span id="LC6514" 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;">nonmale_missing_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">missing_male_<span class="idiff left right">bitvec</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">);</span></span>
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6478
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6515
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<pre style="margin: 0;"> <span id="LC6515" 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;">nonmale_missing_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;">nonmale_missing_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nonmale_missing_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nonmale_missing_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6479
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<td class="diff-line-num new_line old" data-linenumber="6516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6479" 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;">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;">missing_male_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_male_acc1</span>_bits</span><span class="p">);</span></span>
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6516
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<pre style="margin: 0;">+<span id="LC6516" 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;">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;">missing_male_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_male</span>_bits</span><span class="p">);</span></span>
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6480
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6517
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<pre style="margin: 0;"> <span id="LC6517" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_dosages_vmaj_iter</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing_effect</span><span class="p">;</span></span>
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6481
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6518
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<pre style="margin: 0;"> <span id="LC6518" class="line" lang="cpp"> <span class="p">}</span></span>
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6482
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6519
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<pre style="margin: 0;"> <span id="LC6519" class="line" lang="cpp"> <span class="p">}</span></span>
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6483
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6520
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<pre style="margin: 0;"> <span id="LC6520" class="line" lang="cpp"> <span class="p">}</span></span>
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6484
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<td class="diff-line-num new_line" data-linenumber="6521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6521
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<pre style="margin: 0;"> <span id="LC6521" 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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6485
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6522
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<pre style="margin: 0;"> <span id="LC6522" class="line" lang="cpp"> <span class="n" style="color: #333;">missing_effect</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">ploidy_d</span><span class="p">;</span></span>
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6486
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<td class="diff-line-num new_line old" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6486" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_<span class="idiff left">acc1_bits</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">missing_acc1</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6523
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<pre style="margin: 0;">+<span id="LC6523" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_<span class="idiff left">bits</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">missing_bitvec</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6487
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<td class="diff-line-num new_line" data-linenumber="6524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6524
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<pre style="margin: 0;"> <span id="LC6524" 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;">missing_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;">missing_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">missing_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">missing_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6488
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<td class="diff-line-num new_line old" data-linenumber="6525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6488" 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;">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;">missing_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_acc1</span>_bits</span><span class="p">);</span></span>
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6525
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<pre style="margin: 0;">+<span id="LC6525" 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;">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;">missing_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing</span>_bits</span><span class="p">);</span></span>
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6489
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6526
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<pre style="margin: 0;"> <span id="LC6526" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_dosages_vmaj_iter</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing_effect</span><span class="p">;</span></span>
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6490
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6527
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<pre style="margin: 0;"> <span id="LC6527" class="line" lang="cpp"> <span class="p">}</span></span>
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6491
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6528
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<pre style="margin: 0;"> <span id="LC6528" class="line" lang="cpp"> <span class="p">}</span></span>
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6492
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6529
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<pre style="margin: 0;"> <span id="LC6529" class="line" lang="cpp"> <span class="p">}</span></span>
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6493
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6530
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<pre style="margin: 0;"> <span id="LC6530" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">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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6494
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<td class="diff-line-num new_line old" data-linenumber="6531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_<span class="idiff left">acc1_inv_bits</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 right">missing_acc1</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6531
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<pre style="margin: 0;">+<span id="LC6531" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">missing_<span class="idiff left">inv_bits</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 right">missing_bitvec</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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6495
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<td class="diff-line-num new_line" data-linenumber="6532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6532
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<pre style="margin: 0;"> <span id="LC6532" 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;">nm_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;">nm_sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nm_sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6496
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<td class="diff-line-num new_line old" data-linenumber="6533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6496" 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;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter0</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">acc1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing_acc1</span>_inv_bits</span><span class="p">);</span></span>
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6533
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<pre style="margin: 0;">+<span id="LC6533" 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;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter0</span><span class="p">(</span><span class="n" style="color: #333;">missing_<span class="idiff left">bitvec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">sample_idx_base</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">missing</span>_inv_bits</span><span class="p">);</span></span>
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6497
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6534
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<pre style="margin: 0;"> <span id="LC6534" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_dosages_vmaj_iter</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">u63tod</span><span class="p">(</span><span class="n" style="color: #333;">ddosage_incrs</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">geno_slope</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno_intercept</span><span class="p">;</span></span>
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6498
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6535
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<pre style="margin: 0;"> <span id="LC6535" class="line" lang="cpp"> <span class="p">}</span></span>
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6499
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6536
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<pre style="margin: 0;"> <span id="LC6536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">se_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6570" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6533,7 +6570,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6533
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<td class="diff-line-num new_line" data-linenumber="6570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6570
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<pre style="margin: 0;"> <span id="LC6570" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_score_coefs_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;">cur_score_coefs_iter</span><span class="p">[</span><span class="n" style="color: #333;">kScoreVariantBlockSize</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6534
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<td class="diff-line-num new_line" data-linenumber="6571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6571
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<pre style="margin: 0;"> <span id="LC6571" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6535
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<td class="diff-line-num new_line" data-linenumber="6572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6572
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<pre style="margin: 0;"> <span id="LC6572" 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;">bit_idx_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RawToSubsettedPos</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include_cumulative_popcounts</span><span class="p">,</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6536
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<td class="diff-line-num new_line old" data-linenumber="6573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6536" 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;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6573
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<pre style="margin: 0;">+<span id="LC6573" 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;">uint<span class="idiff left right">ptr</span>_t</span> <span class="n" style="color: #333;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6537
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<td class="diff-line-num new_line" data-linenumber="6574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6574
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<pre style="margin: 0;"> <span id="LC6574" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cur_coef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_coef</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">u31tod</span><span class="p">(</span><span class="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">qsr_include</span><span class="p">,</span> <span class="n" style="color: #333;">qsr_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bit_idx_base</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="6538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6538
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<td class="diff-line-num new_line" data-linenumber="6575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6575
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<pre style="margin: 0;"> <span id="LC6575" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_score_coefs_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_coef</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6539
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<td class="diff-line-num new_line" data-linenumber="6576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6576
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<pre style="margin: 0;"> <span id="LC6576" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_score_coefs_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;">cur_score_coefs_iter</span><span class="p">[</span><span class="n" style="color: #333;">kScoreVariantBlockSize</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6579" style="width: 35px; color: rgba(0,0,0,0.3); 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="6616" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6579,10 +6616,18 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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<td class="diff-line-num old_line" data-linenumber="6579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6579
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<td class="diff-line-num new_line" data-linenumber="6616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6616
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<pre style="margin: 0;"> <span id="LC6616" 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;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">score_txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6580
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<td class="diff-line-num new_line" data-linenumber="6617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6617
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<pre style="margin: 0;"> <span id="LC6617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">ScoreReport_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6581
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<td class="diff-line-num new_line" data-linenumber="6618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6618
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<pre style="margin: 0;"> <span id="LC6618" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6582
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<td class="diff-line-num new_line old" data-linenumber="6619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6582" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr4To8</span><span class="p">(</span><span class="n" style="color: #333;">missing_diploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6583
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<td class="diff-line-num new_line old" data-linenumber="6619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6583" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr8To32</span><span class="p">(</span><span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc32</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6584
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<td class="diff-line-num new_line old" data-linenumber="6619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6584" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr4To8</span><span class="p">(</span><span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6585
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<td class="diff-line-num new_line old" data-linenumber="6619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6585" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr8To32</span><span class="p">(</span><span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc32</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6619
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<pre style="margin: 0;">+<span id="LC6619" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6620
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<pre style="margin: 0;">+<span id="LC6620" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc4</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;">missing_accx</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_idx</span><span class="p">]);</span></span>
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6621
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<pre style="margin: 0;">+<span id="LC6621" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc8</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;">missing_diploid_acc4</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">]);</span></span>
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6622
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<pre style="margin: 0;">+<span id="LC6622" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_diploid_acc32</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;">missing_diploid_acc8</span><span class="p">[</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">]);</span></span>
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6623
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<pre style="margin: 0;">+<span id="LC6623" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc4</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;">missing_male_accx</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qsr_idx</span><span class="p">]);</span></span>
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6624
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<pre style="margin: 0;">+<span id="LC6624" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc8</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;">missing_haploid_acc4</span><span class="p">[</span><span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">]);</span></span>
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6625
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<pre style="margin: 0;">+<span id="LC6625" class="line" lang="cpp"> <span class="n" style="color: #333;">VecW</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">missing_haploid_acc32</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;">missing_haploid_acc8</span><span class="p">[</span><span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">]);</span></span>
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6626
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<pre style="margin: 0;">+<span id="LC6626" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr4To8</span><span class="p">(</span><span class="n" style="color: #333;">missing_diploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">);</span></span>
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6627
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<pre style="margin: 0;">+<span id="LC6627" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr8To32</span><span class="p">(</span><span class="n" style="color: #333;">missing_diploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_diploid_acc32</span><span class="p">);</span></span>
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6628
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<pre style="margin: 0;">+<span id="LC6628" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr4To8</span><span class="p">(</span><span class="n" style="color: #333;">missing_haploid_acc4</span><span class="p">,</span> <span class="n" style="color: #333;">acc4_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">);</span></span>
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6629
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<pre style="margin: 0;">+<span id="LC6629" class="line" lang="cpp"> <span class="n" style="color: #333;">VcountIncr8To32</span><span class="p">(</span><span class="n" style="color: #333;">missing_haploid_acc8</span><span class="p">,</span> <span class="n" style="color: #333;">acc8_vec_ct</span><span class="p">,</span> <span class="n" style="color: #333;">missing_haploid_acc32</span><span class="p">);</span></span>
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6630
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<pre style="margin: 0;">+<span id="LC6630" class="line" lang="cpp"> <span class="p">}</span></span>
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6586
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6631
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<pre style="margin: 0;"> <span id="LC6631" 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_not_first_block</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ThreadsAreActive</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tg</span><span class="p">);</span></span>
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6587
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6632
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<pre style="margin: 0;"> <span id="LC6632" class="line" lang="cpp"> <span class="n" style="color: #333;">putc_unlocked</span><span class="p">(</span><span class="sc" style="color: #d14;">'\r'</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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6588
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6633
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<pre style="margin: 0;"> <span id="LC6633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">missing_var_id_ct</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">missing_allele_code_ct</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">duplicated_var_id_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="6644" style="width: 35px; color: rgba(0,0,0,0.3); 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="6689" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6644,8 +6689,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6644
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6689
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<pre style="margin: 0;"> <span id="LC6689" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Variant list written to %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;">outname</span><span class="p">);</span></span>
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6645
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6690
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<pre style="margin: 0;"> <span id="LC6690" class="line" lang="cpp"> <span class="p">}</span></span>
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6646
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6691
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<pre style="margin: 0;"> <span id="LC6691" class="line" lang="cpp"></span>
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6647
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<pre style="margin: 0;">-<span id="LC6647" 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;">qsr_ct_nz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qsr_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">qsr_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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6648
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<pre style="margin: 0;">-<span id="LC6648" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6692
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<pre style="margin: 0;">+<span id="LC6692" 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;">qsr_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;">qsr_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">qsr_ct_nz</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qsr_idx</span><span class="p">)</span> <span class="p">{</span></span>
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6649
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6693
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<pre style="margin: 0;"> <span id="LC6693" 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;">outname_end2</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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6650
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6694
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<pre style="margin: 0;"> <span id="LC6694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">range_names</span><span class="p">)</span> <span class="p">{</span></span>
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6651
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6695
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<pre style="margin: 0;"> <span id="LC6695" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outname_end2</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6720" style="width: 35px; color: rgba(0,0,0,0.3); 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="6764" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6720,8 +6764,8 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6720
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6764
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<pre style="margin: 0;"> <span id="LC6764" class="line" lang="cpp"> <span class="p">}</span></span>
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6721
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6765
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<pre style="margin: 0;"> <span id="LC6765" class="line" lang="cpp"> <span class="p">}</span></span>
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6722
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6766
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<pre style="margin: 0;"> <span id="LC6766" class="line" lang="cpp"> <span class="n" style="color: #333;">AppendBinaryEoln</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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6723
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<pre style="margin: 0;">-<span id="LC6723" 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;">scrambled_missing_diploid_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">R_CAST</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_diploid_acc32</span></span><span class="p">);</span></span>
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6724
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<td class="diff-line-num new_line old" data-linenumber="6767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6724" 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;">scrambled_missing_haploid_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">R_CAST</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">missing_haploid_acc32</span></span><span class="p">);</span></span>
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6767
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<pre style="margin: 0;">+<span id="LC6767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">scrambled_missing_diploid_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">R_CAST</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">missing_accx</span></span><span class="p"><span class="idiff">)[</span></span><span class="n" style="color: #333;"><span class="idiff">acc4_vec_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="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</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">qsr_idx</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">kInt32PerVec</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6768
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<pre style="margin: 0;">+<span id="LC6768" class="line" lang="cpp"> <span class="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;">scrambled_missing_haploid_cts</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">R_CAST</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">missing_male_accx</span></span><span class="p"><span class="idiff">)[</span></span><span class="n" style="color: #333;"><span class="idiff">acc4_vec_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="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">11</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">qsr_idx</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">kInt32PerVec</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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6725
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6769
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<pre style="margin: 0;"> <span id="LC6769" 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;">output_missing_pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_output_missing_pheno</span><span class="p">;</span></span>
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6726
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6770
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<pre style="margin: 0;"> <span id="LC6770" 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;">omp_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;">output_missing_pheno</span><span class="p">);</span></span>
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6727
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6771
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<pre style="margin: 0;"> <span id="LC6771" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6813" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6769,7 +6813,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6769
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6813
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<pre style="margin: 0;"> <span id="LC6813" 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;">output_missing_pheno</span><span class="p">,</span> <span class="n" style="color: #333;">omp_slen</span><span class="p">);</span></span>
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6770
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<td class="diff-line-num new_line" data-linenumber="6814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6814
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<pre style="margin: 0;"> <span id="LC6814" class="line" lang="cpp"> <span class="p">}</span></span>
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6771
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<td class="diff-line-num new_line" data-linenumber="6815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6815
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<pre style="margin: 0;"> <span id="LC6815" 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;">scrambled_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VcountScramble1</span><span class="p">(</span><span class="n" style="color: #333;">sample_idx</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6772
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<td class="diff-line-num new_line old" data-linenumber="6816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6772" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_ct_base</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IsSet</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_uidx</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">male_allele_ct_delta</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6816
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<pre style="margin: 0;">+<span id="LC6816" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele_ct_base<span class="idiff left">s</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">qsr_idx</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">IsSet</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample_uidx</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">male_allele_ct_deltas</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">qsr_idx</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6773
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<td class="diff-line-num new_line" data-linenumber="6817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6817
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<pre style="margin: 0;"> <span id="LC6817" 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;">nallele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">denom</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;">scrambled_missing_diploid_cts</span><span class="p">[</span><span class="n" style="color: #333;">scrambled_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">scrambled_missing_haploid_cts</span><span class="p">[</span><span class="n" style="color: #333;">scrambled_idx</span><span class="p">];</span></span>
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6774
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<td class="diff-line-num new_line" data-linenumber="6818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6818
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<pre style="margin: 0;"> <span id="LC6818" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_nallele</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6775
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<td class="diff-line-num new_line" data-linenumber="6819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6819
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<pre style="margin: 0;"> <span id="LC6819" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6784" style="width: 35px; color: rgba(0,0,0,0.3); 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="6828" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6784,7 +6828,7 @@ PglErr ScoreReport(const uintptr_t* sample_include, const SampleIdInfo* siip, co</td>
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6784
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6828
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<pre style="margin: 0;"> <span id="LC6828" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6785
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<td class="diff-line-num new_line" data-linenumber="6829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6829
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<pre style="margin: 0;"> <span id="LC6829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_dosage_sum</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6786
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<td class="diff-line-num new_line" data-linenumber="6830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6830
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<pre style="margin: 0;"> <span id="LC6830" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6787
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<td class="diff-line-num new_line old" data-linenumber="6831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6787" 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;">ddosagetoa</span><span class="p">(</span><span class="n" style="color: #333;">ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">],</span> <span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6831
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<pre style="margin: 0;">+<span id="LC6831" 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;">ddosagetoa</span><span class="p">(</span><span class="n" style="color: #333;">ddosage_sums</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qsr_idx</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">sample_ct</span></span><span class="p">],</span> <span class="n" style="color: #333;">cswritep</span><span class="p">);</span></span>
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6788
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<td class="diff-line-num new_line" data-linenumber="6832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6832
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<pre style="margin: 0;"> <span id="LC6832" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6789
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<td class="diff-line-num new_line" data-linenumber="6833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6833
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<pre style="margin: 0;"> <span id="LC6833" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">final_score_col</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;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">final_scores_cmaj</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6790
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<td class="diff-line-num new_line" data-linenumber="6834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6834
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<pre style="margin: 0;"> <span id="LC6834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_score_avgs</span><span class="p">)</span> <span class="p">{</span></span>
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