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<h3>
Dylan Aïssi 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/394d8a281efdc53907dca6c9cc8dbb8c15317766">394d8a28</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-04-21T09:10:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-200409+dfsg</pre>
</li>
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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="#49a9b8ad832d31a64af7997ab4dff296fe4603bc">
plink2_data.cc
</a>
</li>
<li class="file-stats">
<a href="#a125279a9188813c60a6fe3d56cead0bd36fcc8f">
plink2_data.h
</a>
</li>
<li class="file-stats">
<a href="#82c8c0946825d16815c68e845955a90079d70b6b">
plink2_glm.cc
</a>
</li>
<li class="file-stats">
<a href="#2a4cda92f206bc9a46e7c7168314aa0fad145d68">
plink2_glm.h
</a>
</li>
<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/394d8a281efdc53907dca6c9cc8dbb8c15317766#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f"><strong>plink2.cc</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -66,10 +66,10 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_MKL</span></span>
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67
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67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="s" style="color: #d14;">" Intel"</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (<span class="idiff left right">21 Ma</span>r 2020)"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="s" style="color: #d14;">" (<span class="idiff left right">9 Ap</span>r 2020)"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">""</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="s" style="color: #d14;">"<span class="idiff left right"> </span>"</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef LAPACK_ILP64</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="s" style="color: #d14;">" "</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5171" style="width: 35px; color: rgba(0,0,0,0.3); 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="5171" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5171,6 +5171,7 @@ int main(int argc, char** argv) {</td>
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5171
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5171
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<pre style="margin: 0;"> <span id="LC5171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_2A</span><span class="p">;</span></span>
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5172
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5172
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<pre style="margin: 0;"> <span id="LC5172" class="line" lang="cpp"> <span class="p">}</span></span>
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5173
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5173
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<pre style="margin: 0;"> <span id="LC5173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">explicit_firth_fallback</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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5174
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<pre style="margin: 0;">+<span id="LC5174" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">glm_allow_no_covars</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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5174
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5175
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<pre style="margin: 0;"> <span id="LC5175" 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;">param_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">param_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">param_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">param_idx</span><span class="p">)</span> <span class="p">{</span></span>
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5175
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5176
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<pre style="margin: 0;"> <span id="LC5176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_modif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">];</span></span>
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5176
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<td class="diff-line-num new_line" data-linenumber="5177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5177
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_modif_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;">cur_modif</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5313,7 +5314,7 @@ int main(int argc, char** argv) {</td>
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5313
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<td class="diff-line-num new_line" data-linenumber="5314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5314
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<pre style="margin: 0;"> <span id="LC5314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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5314
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<td class="diff-line-num new_line" data-linenumber="5315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5315
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<pre style="margin: 0;"> <span id="LC5315" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="5315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5315
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<td class="diff-line-num new_line" data-linenumber="5316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5316
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<pre style="margin: 0;"> <span id="LC5316" class="line" lang="cpp"> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">glm_info</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;">kfGlmLocalCats1based</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5316
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<td class="diff-line-num new_line old" data-linenumber="5317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5316" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">likely</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">StrStartsWith</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cur_modif</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"local-cats0="</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cur_modif_slen</span></span><span class="p"><span class="idiff right">)</span>))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5317" style="width: 35px; color: rgba(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="5317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5317
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<pre style="margin: 0;">+<span id="LC5317" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">StrStartsWith</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cur_modif</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"local-cats0="</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cur_modif_slen</span></span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5317
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<td class="diff-line-num new_line" data-linenumber="5318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5318
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<pre style="margin: 0;"> <span id="LC5318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">glm_info</span><span class="p">.</span><span class="n" style="color: #333;">local_cat_ct</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5318
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<td class="diff-line-num new_line" data-linenumber="5319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5319
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5319" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Multiple --glm local-cats[0]= modifiers.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5319
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<td class="diff-line-num new_line" data-linenumber="5320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5320
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<pre style="margin: 0;"> <span id="LC5320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5322" style="width: 35px; color: rgba(0,0,0,0.3); 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="5323" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5322,6 +5323,8 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="5322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5322
</td>
<td class="diff-line-num new_line" data-linenumber="5323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5323
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5323" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Invalid --glm local-cats0= category count (must be in [2, 4095]).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5323
</td>
<td class="diff-line-num new_line" data-linenumber="5324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5324
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5324
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<td class="diff-line-num new_line" data-linenumber="5325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5325
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<pre style="margin: 0;"> <span id="LC5325" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="5326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5326
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5326" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likely</span><span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"allow-no-covars"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="5327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5327
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5327" class="line" lang="cpp"> <span class="n" style="color: #333;">glm_allow_no_covars</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5325
</td>
<td class="diff-line-num new_line" data-linenumber="5328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5328
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5328" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5326
</td>
<td class="diff-line-num new_line" data-linenumber="5329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5329
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5329" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Invalid --glm argument '%s'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5327
</td>
<td class="diff-line-num new_line" data-linenumber="5330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5330
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_WWA</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5371" style="width: 35px; color: rgba(0,0,0,0.3); 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="5374" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5371,6 +5374,10 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="5371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5371
</td>
<td class="diff-line-num new_line" data-linenumber="5374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5374
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<pre style="margin: 0;"> <span id="LC5374" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --glm 'local-cats[0]=' must be used with 'local-covar='.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="5372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5372
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<td class="diff-line-num new_line" data-linenumber="5375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5375
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<pre style="margin: 0;"> <span id="LC5375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5373
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<td class="diff-line-num new_line" data-linenumber="5376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5376
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<pre style="margin: 0;"> <span id="LC5376" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5374" style="width: 35px; color: rgba(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="5377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5377
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<pre style="margin: 0;">+<span id="LC5377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">covar_fname</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;">pc</span><span class="p">.</span><span class="n" style="color: #333;">covar_range_list</span><span class="p">.</span><span class="n" style="color: #333;">name_ct</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;">glm_allow_no_covars</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5374" style="width: 35px; color: rgba(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="5378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5378
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<pre style="margin: 0;">+<span id="LC5378" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --glm invoked without --covar/--covar-name/--covar-col-nums; this is</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">usually an analytical mistake. Add the 'allow-no-covars' modifier if you are</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">sure you want this.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5374" style="width: 35px; color: rgba(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="5379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5379
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<pre style="margin: 0;">+<span id="LC5379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5374" style="width: 35px; color: rgba(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="5380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5380
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<pre style="margin: 0;">+<span id="LC5380" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="5374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5374
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<td class="diff-line-num new_line" data-linenumber="5381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5381
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<pre style="margin: 0;"> <span id="LC5381" 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="5375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5375
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<td class="diff-line-num new_line" data-linenumber="5382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5382
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">glm_local_pvar_fname</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pc</span><span class="p">.</span><span class="n" style="color: #333;">glm_info</span><span class="p">.</span><span class="n" style="color: #333;">local_first_covar_col</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5376
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<td class="diff-line-num new_line" data-linenumber="5383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5383
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5383" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --glm local-pvar= and local-pos-cols= cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6305" style="width: 35px; color: rgba(0,0,0,0.3); 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="6312" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6305,7 +6312,7 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="6305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6305
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<td class="diff-line-num new_line" data-linenumber="6312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6312
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<pre style="margin: 0;"> <span id="LC6312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">EnforceParamCtRange</span><span class="p">(</span><span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span><span class="p">],</span> <span class="n" style="color: #333;">param_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6306
</td>
<td class="diff-line-num new_line" data-linenumber="6313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6313
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_2A</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6307
</td>
<td class="diff-line-num new_line" data-linenumber="6314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6314
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6314" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6308
</td>
<td class="diff-line-num new_line old" data-linenumber="6315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6308" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="6315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6315
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<pre style="margin: 0;">+<span id="LC6315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6309
</td>
<td class="diff-line-num new_line" data-linenumber="6316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6316
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<pre style="margin: 0;"> <span id="LC6316" 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;">param_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">param_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">param_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">param_idx</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6310
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<td class="diff-line-num new_line" data-linenumber="6317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6317
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_modif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">];</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6311
</td>
<td class="diff-line-num new_line" data-linenumber="6318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6318
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_modif_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;">cur_modif</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6355" style="width: 35px; color: rgba(0,0,0,0.3); 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="6362" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6355,14 +6362,14 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="6355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6355
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6362
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<pre style="margin: 0;"> <span id="LC6362" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2TrimAlts</span><span class="p">;</span></span>
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6356
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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 class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-alt2+"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6357
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6364
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<pre style="margin: 0;"> <span id="LC6364" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2EraseAlt2Plus</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="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-split"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6359
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<pre style="margin: 0;">-<span id="LC6359" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</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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6360
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<pre style="margin: 0;">-<span id="LC6360" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-split-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6361
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<td class="diff-line-num new_line old" data-linenumber="6365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6361" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</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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6362
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<pre style="margin: 0;">-<span id="LC6362" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-join"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6363
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<pre style="margin: 0;">-<span id="LC6363" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</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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6364
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<pre style="margin: 0;">-<span id="LC6364" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6365
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<pre style="margin: 0;">-<span id="LC6365" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidDup</span><span class="p">;</span></span>
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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 class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-split"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6366
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<pre style="margin: 0;">+<span id="LC6366" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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6367
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<pre style="margin: 0;">+<span id="LC6367" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-split-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6368
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<pre style="margin: 0;">+<span id="LC6368" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-join"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6370
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<pre style="margin: 0;">+<span id="LC6370" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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6371
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<pre style="margin: 0;">+<span id="LC6371" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6372
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<pre style="margin: 0;">+<span id="LC6372" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span><span class="p">;</span></span>
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6366
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6373
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<pre style="margin: 0;"> <span id="LC6373" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-phase"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6367
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6374
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<pre style="margin: 0;"> <span id="LC6374" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePgenErasePhase</span><span class="p">;</span></span>
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6368
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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 class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likely</span><span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-dosage"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6376,29 +6383,29 @@ int main(int argc, char** argv) {</td>
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6376
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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;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'trim-alts' and 'erase-alt2+' modifiers cannot be used</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6377
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6384
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<pre style="margin: 0;"> <span id="LC6384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6378
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6385
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<pre style="margin: 0;"> <span id="LC6385" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">vid_semicolon</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="6386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">idDup</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vid_semicolon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">v</span>id_semicolon</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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6381
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<pre style="margin: 0;">-<span id="LC6381" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left">id-split', 'vid-split-dup', 'vid-dup', and 'vid-join'</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">modifiers are mutually exclusive.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6386
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<pre style="margin: 0;">+<span id="LC6386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span><span class="p">)</span> <span class="p">{</span></span>
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6387
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<pre style="margin: 0;">+<span id="LC6387" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">aridDup</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">varid_semicolon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">var</span>id_semicolon</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6388
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<pre style="margin: 0;">+<span id="LC6388" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left">arid-split', 'varid-split-dup', 'varid-dup', and</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'varid-join' </span>modifiers are mutually exclusive.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6382
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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;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6383
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6390
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<pre style="margin: 0;"> <span id="LC6390" 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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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6391
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<pre style="margin: 0;">+<span id="LC6391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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6385
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6392
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<pre style="margin: 0;"> <span id="LC6392" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MMask</span><span class="p">))))</span> <span class="p">{</span></span>
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6386
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<pre style="margin: 0;">-<span id="LC6386" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left right">id-split' must be used with a multiallelics= split </span>mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6393
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<pre style="margin: 0;">+<span id="LC6393" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left">arid-split' must be used with a multiallelics= split</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6387
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<td class="diff-line-num new_line" data-linenumber="6394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6394
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<pre style="margin: 0;"> <span id="LC6394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6388
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6395
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<pre style="margin: 0;"> <span id="LC6395" class="line" lang="cpp"> <span class="p">}</span></span>
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6389
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<td class="diff-line-num new_line" data-linenumber="6396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6396
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<pre style="margin: 0;"> <span id="LC6396" 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="6390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6390
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<td class="diff-line-num new_line" data-linenumber="6397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6397
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<pre style="margin: 0;"> <span id="LC6397" 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="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</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="6398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'vid-join' must be used with a multiallelics= join mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new 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;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left right">ar</span>id-join' must be used with a multiallelics= join mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6392
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6399
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<pre style="margin: 0;"> <span id="LC6399" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6393
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6400
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<pre style="margin: 0;"> <span id="LC6400" class="line" lang="cpp"> <span class="p">}</span></span>
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6394
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6401
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<pre style="margin: 0;"> <span id="LC6401" class="line" lang="cpp"> <span class="p">}</span></span>
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6395
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<pre style="margin: 0;">-<span id="LC6395" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidSemicolon</span><span class="p">;</span></span>
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6396
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<td class="diff-line-num new_line old" data-linenumber="6402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6397
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<td class="diff-line-num new_line old" data-linenumber="6402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6397" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidDup</span><span class="p">;</span></span>
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6402
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<pre style="margin: 0;">+<span id="LC6402" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idSemicolon</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span><span class="p">;</span></span>
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6398
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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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6399
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<td class="diff-line-num new_line old" data-linenumber="6406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2VidDup</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6406
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<pre style="margin: 0;">+<span id="LC6406" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span><span class="p">)</span> <span class="p">{</span></span>
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6400
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<td class="diff-line-num new_line" data-linenumber="6407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6407
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<pre style="margin: 0;"> <span id="LC6407" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MMask</span><span class="p">))))</span> <span class="p">{</span></span>
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6401
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<td class="diff-line-num new_line old" data-linenumber="6408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6401" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'vid-dup' must be used with a multiallelics= split mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="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">
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<td class="diff-line-num new new_line" data-linenumber="6408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6408
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<pre style="margin: 0;">+<span id="LC6408" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-bpgen 'v<span class="idiff left right">ar</span>id-dup' must be used with a multiallelics= split mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6402
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<td class="diff-line-num new_line" data-linenumber="6409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6409
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<pre style="margin: 0;"> <span id="LC6409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6403
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<td class="diff-line-num new_line" data-linenumber="6410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6410
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<pre style="margin: 0;"> <span id="LC6410" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6404
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<td class="diff-line-num new_line" data-linenumber="6411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6411
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<pre style="margin: 0;"> <span id="LC6411" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6423" style="width: 35px; color: rgba(0,0,0,0.3); 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="6430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6423,7 +6430,7 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="6423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6423
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<td class="diff-line-num new_line" data-linenumber="6430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6430
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<pre style="margin: 0;"> <span id="LC6430" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6424
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<td class="diff-line-num new_line" data-linenumber="6431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6431
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<pre style="margin: 0;"> <span id="LC6431" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">explicit_pvar_cols</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="6425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6425
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<td class="diff-line-num new_line" data-linenumber="6432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6432
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<pre style="margin: 0;"> <span id="LC6432" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">explicit_psam_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6426
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<td class="diff-line-num new_line old" data-linenumber="6433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6427" style="width: 35px; color: rgba(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="6433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6433
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<pre style="margin: 0;">+<span id="LC6433" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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="6427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6427
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<td class="diff-line-num new_line" data-linenumber="6434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6434
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<pre style="margin: 0;"> <span id="LC6434" 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;">param_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">param_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">param_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">param_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6428
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<td class="diff-line-num new_line" data-linenumber="6435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6435
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<pre style="margin: 0;"> <span id="LC6435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_modif</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argvk</span><span class="p">[</span><span class="n" style="color: #333;">arg_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">param_idx</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="6429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6429
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<td class="diff-line-num new_line" data-linenumber="6436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6436
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<pre style="margin: 0;"> <span id="LC6436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_modif_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;">cur_modif</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="6493" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6486,14 +6493,14 @@ int main(int argc, char** argv) {</td>
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6486
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<td class="diff-line-num new_line" data-linenumber="6493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6493
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<pre style="margin: 0;"> <span id="LC6493" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2TrimAlts</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6487
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<td class="diff-line-num new_line" data-linenumber="6494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6494
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<pre style="margin: 0;"> <span id="LC6494" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-alt2+"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6488
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<td class="diff-line-num new_line" data-linenumber="6495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6495
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<pre style="margin: 0;"> <span id="LC6495" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2EraseAlt2Plus</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" 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">
6489
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<td class="diff-line-num new_line old" data-linenumber="6496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6489" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-split"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6490
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<td class="diff-line-num new_line old" data-linenumber="6496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6490" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">|=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6491
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<pre style="margin: 0;">-<span id="LC6491" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-split-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6492
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<pre style="margin: 0;">-<span id="LC6492" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</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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6493
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<pre style="margin: 0;">-<span id="LC6493" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-join"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6494
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<pre style="margin: 0;">-<span id="LC6494" class="line" lang="cpp"> <span class="n" style="color: #333;">vid_semicolon</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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6495
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<pre style="margin: 0;">-<span id="LC6495" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"vid-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6496
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<pre style="margin: 0;">-<span id="LC6496" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidDup</span><span class="p">;</span></span>
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6496
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<pre style="margin: 0;">+<span id="LC6496" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-split"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6497
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<pre style="margin: 0;">+<span id="LC6497" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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6498
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<pre style="margin: 0;">+<span id="LC6498" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-split-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6499
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<pre style="margin: 0;">+<span id="LC6499" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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6500
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<pre style="margin: 0;">+<span id="LC6500" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-join"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6501
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<pre style="margin: 0;">+<span id="LC6501" class="line" lang="cpp"> <span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</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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6502
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<pre style="margin: 0;">+<span id="LC6502" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"v<span class="idiff left right">ar</span>id-dup"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6503
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<pre style="margin: 0;">+<span id="LC6503" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span><span class="p">;</span></span>
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6497
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6504
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<pre style="margin: 0;"> <span id="LC6504" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-phase"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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6498
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6505
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<pre style="margin: 0;"> <span id="LC6505" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePgenErasePhase</span><span class="p">;</span></span>
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6499
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6506
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<pre style="margin: 0;"> <span id="LC6506" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">cur_modif</span><span class="p">,</span> <span class="s" style="color: #d14;">"erase-dosage"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_modif_slen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6517" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6517,25 +6524,25 @@ int main(int argc, char** argv) {</td>
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6517
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6524
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<pre style="margin: 0;"> <span id="LC6524" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'trim-alts' and 'erase-alt2+' modifiers cannot be used</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6518
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<td class="diff-line-num new_line" data-linenumber="6525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6525
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<pre style="margin: 0;"> <span id="LC6525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6519
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<td class="diff-line-num new_line" data-linenumber="6526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6526
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<pre style="margin: 0;"> <span id="LC6526" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6520
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<td class="diff-line-num new_line old" data-linenumber="6527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_semicolon</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6521
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<td class="diff-line-num new_line old" data-linenumber="6527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6521" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">idDup</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vid_semicolon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">v</span>id_semicolon</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6522
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<td class="diff-line-num new_line old" data-linenumber="6527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6522" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'v<span class="idiff left">id-split', 'vid-split-dup', 'vid-dup', and 'vid-join'</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">modifiers are mutually exclusive.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6527
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<pre style="margin: 0;">+<span id="LC6527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6528
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<pre style="margin: 0;">+<span id="LC6528" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">aridDup</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">varid_semicolon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">var</span>id_semicolon</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="6529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6529
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6529" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'v<span class="idiff left">arid-split', 'varid-split-dup', 'varid-dup', and</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'varid-join' </span>modifiers are mutually exclusive.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6523
</td>
<td class="diff-line-num new_line" data-linenumber="6530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6530
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6524
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<td class="diff-line-num new_line" data-linenumber="6531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6531
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6531" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" 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">
6525
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<td class="diff-line-num new_line old" data-linenumber="6532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6526" style="width: 35px; color: rgba(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="6532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6532
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<pre style="margin: 0;">+<span id="LC6532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6526
</td>
<td class="diff-line-num new_line" data-linenumber="6533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6533
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6533" 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;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MMask</span><span class="p">))))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6527
</td>
<td class="diff-line-num new_line old" data-linenumber="6534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6527" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'vid-split' must be used with a multiallelics= split mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="6534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6534
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6534" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'v<span class="idiff left right">ar</span>id-split' must be used with a multiallelics= split mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6528
</td>
<td class="diff-line-num new_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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6529
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<td class="diff-line-num new_line" data-linenumber="6536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6536
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6536" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6530
</td>
<td class="diff-line-num new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6537" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6531
</td>
<td class="diff-line-num new_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
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6538" 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="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6532
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<pre style="margin: 0;">-<span id="LC6532" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'vid-join' must be used with a multiallelics= join mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6539
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<pre style="margin: 0;">+<span id="LC6539" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --make-pgen 'v<span class="idiff left right">ar</span>id-join' must be used with a multiallelics= join mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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6533
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6540
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<pre style="margin: 0;"> <span id="LC6540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6534
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6541
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<pre style="margin: 0;"> <span id="LC6541" class="line" lang="cpp"> <span class="p">}</span></span>
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6535
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<td class="diff-line-num new_line" data-linenumber="6542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6542
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<pre style="margin: 0;"> <span id="LC6542" class="line" lang="cpp"> <span class="p">}</span></span>
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6536
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<td class="diff-line-num new_line old" data-linenumber="6543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidSemicolon</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6537
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<td class="diff-line-num new_line old" data-linenumber="6543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_semicolon</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6538
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<td class="diff-line-num new_line old" data-linenumber="6543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6538" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2VidDup</span><span class="p">;</span></span>
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6543
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<pre style="margin: 0;">+<span id="LC6543" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idSemicolon</span><span class="p">;</span></span>
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6544
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<pre style="margin: 0;">+<span id="LC6544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_semicolon</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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6545
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<pre style="margin: 0;">+<span id="LC6545" class="line" lang="cpp"> <span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span><span class="p">;</span></span>
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6539
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6546
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<pre style="margin: 0;"> <span id="LC6546" class="line" lang="cpp"> <span class="p">}</span></span>
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6540
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6547
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<pre style="margin: 0;"> <span id="LC6547" class="line" lang="cpp"> <span class="p">}</span></span>
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6541
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6548
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<pre style="margin: 0;"> <span id="LC6548" 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;">explicit_pvar_cols</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="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3218,7 +3218,7 @@ PglErr PlanMultiallelicSplit(const uintptr_t* variant_include, const uintptr_t*</td>
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3218
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3218
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<pre style="margin: 0;"> <span id="LC3218" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3219
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<td class="diff-line-num new_line" data-linenumber="3219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3219
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<pre style="margin: 0;"> <span id="LC3219" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Returns 1 iff there are exactly (allele_ct - 2) semicolons in</span></span>
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<td class="diff-line-num old_line" data-linenumber="3220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3220
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3220
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<pre style="margin: 0;"> <span id="LC3220" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// orig_variant_id, and no two are adjacent (or leading/trailing).</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3221
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<pre style="margin: 0;">-<span id="LC3221" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">VidSplitOk</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;">orig_variant_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">)</span> <span class="p">{</span></span>
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3221
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<pre style="margin: 0;">+<span id="LC3221" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">V<span class="idiff left right">ar</span>idSplitOk</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;">orig_variant_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">)</span> <span class="p">{</span></span>
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3222
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3222
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<pre style="margin: 0;"> <span id="LC3222" 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;">id_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3223
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3223
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<pre style="margin: 0;"> <span id="LC3223" 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;">aidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">aidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">allele_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">aidx</span><span class="p">)</span> <span class="p">{</span></span>
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3224
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<pre style="margin: 0;"> <span id="LC3224" 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;">tok_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">id_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">';'</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">@@ -3233,7 +3233,7 @@ uint32_t VidSplitOk(const char* orig_variant_id, uint32_t allele_ct) {</td>
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3233
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3233
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<pre style="margin: 0;"> <span id="LC3233" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Similar to WriteMapOrBim(), but there are enough small differences to</span></span>
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3234
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3234
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<pre style="margin: 0;"> <span id="LC3234" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// justify making this a separate function instead of clogging the original</span></span>
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3235
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3235
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<pre style="margin: 0;"> <span id="LC3235" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// with more conditionals.</span></span>
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<pre style="margin: 0;">-<span id="LC3236" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteBimSplit</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">varid_template_str</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;">missing_varid_match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v<span class="idiff left">id_split</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">v</span>id_dup</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">output_zst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">thread_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3236" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteBimSplit</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">varid_template_str</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;">missing_varid_match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">v<span class="idiff left">arid_split</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">var</span>id_dup</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">output_zst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">thread_ct</span><span class="p">)</span> <span class="p">{</span></span>
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3237
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<pre style="margin: 0;"> <span id="LC3237" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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3238
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3238
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<pre style="margin: 0;"> <span id="LC3238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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3239
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<pre style="margin: 0;"> <span id="LC3239" class="line" lang="cpp"> <span class="n" style="color: #333;">CompressStreamState</span> <span class="n" style="color: #333;">css</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">@@ -3247,7 +3247,7 @@ PglErr WriteBimSplit(const char* outname, const uintptr_t* variant_include, cons</td>
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3247
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3247
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<pre style="margin: 0;"> <span id="LC3247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WriteBimSplit_ret_NOMEM</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3248" class="line" lang="cpp"> <span class="p">}</span></span>
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3249
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<pre style="margin: 0;"> <span id="LC3249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_variant_id_overflow_missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfMiscNewVarIdOverflowMissing</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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3250
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<pre style="margin: 0;">-<span id="LC3250" 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;">v<span class="idiff left">id_dup_nosplit</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">vid_dup</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="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">v</span>id_split</span><span class="p">);</span></span>
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3250
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<pre style="margin: 0;">+<span id="LC3250" 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;">v<span class="idiff left">arid_dup_nosplit</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">varid_dup</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="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">var</span>id_split</span><span class="p">);</span></span>
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3251
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3251
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<pre style="margin: 0;"> <span id="LC3251" class="line" lang="cpp"> <span class="n" style="color: #333;">VaridTemplate</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">varid_templatep</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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3252
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3252
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<pre style="margin: 0;"> <span id="LC3252" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">missing_varid_slen</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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3253
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3253
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<pre style="margin: 0;"> <span id="LC3253" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">missing_varid_match_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// nonzero iff --set-missing-var-ids</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3264" style="width: 35px; color: rgba(0,0,0,0.3); 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="3264" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3264,7 +3264,7 @@ PglErr WriteBimSplit(const char* outname, const uintptr_t* variant_include, cons</td>
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3264
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3264
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<pre style="margin: 0;"> <span id="LC3264" class="line" lang="cpp"> <span class="p">}</span></span>
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3265
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3265
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<pre style="margin: 0;"> <span id="LC3265" 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;">overflow_substitute_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_variant_id_overflow_missing</span><span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">missing_varid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3266
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3266
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<pre style="margin: 0;"> <span id="LC3266" class="line" lang="cpp"> <span class="n" style="color: #333;">VaridTemplateInit</span><span class="p">(</span><span class="n" style="color: #333;">varid_template_str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_varid_match</span><span class="p">,</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">overflow_substitute_blen</span><span class="p">,</span> <span class="n" style="color: #333;">varid_templatep</span><span class="p">);</span></span>
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3267
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<pre style="margin: 0;">-<span id="LC3267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3267
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<pre style="margin: 0;">+<span id="LC3267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3268
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3268
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<pre style="margin: 0;"> <span id="LC3268" 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;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">insert_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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3269
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3269
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<pre style="margin: 0;"> <span id="LC3269" 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;">insert_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">insert_types</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">];</span></span>
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3270
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3270
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<pre style="margin: 0;"> <span id="LC3270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">insert_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">insert_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alleles_needed</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</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="3313" style="width: 35px; color: rgba(0,0,0,0.3); 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="3313" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3313,16 +3313,16 @@ PglErr WriteBimSplit(const char* outname, const uintptr_t* variant_include, cons</td>
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3313
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3313
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<pre style="margin: 0;"> <span id="LC3313" 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;">ref_allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_alleles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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3314
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3314
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<pre style="margin: 0;"> <span id="LC3314" 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;">ref_allele_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;">ref_allele</span><span class="p">);</span></span>
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3315
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3315
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<pre style="margin: 0;"> <span id="LC3315" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">keep_orig_id</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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3316
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<pre style="margin: 0;">-<span id="LC3316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">orig_allele_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">vid_dup_nosplit</span><span class="p">))</span> <span class="p">{</span></span>
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3316
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<pre style="margin: 0;">+<span id="LC3316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">orig_allele_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="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<span class="idiff left right">ar</span>id_dup_nosplit</span><span class="p">))</span> <span class="p">{</span></span>
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3317
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3317
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<pre style="margin: 0;"> <span id="LC3317" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_orig_id</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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3318
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3318
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<pre style="margin: 0;"> <span id="LC3318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">varid_templatep</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;">missing_varid_match_blen</span><span class="p">))</span> <span class="p">{</span></span>
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3319
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3319
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<pre style="margin: 0;"> <span id="LC3319" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_varid_templatep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">varid_templatep</span><span class="p">;</span></span>
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3320
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3320
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<pre style="margin: 0;"> <span id="LC3320" 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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3321
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3321
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<pre style="margin: 0;"> <span id="LC3321" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_varid_templatep</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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3322
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<td class="diff-line-num new_line old" data-linenumber="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_split</span><span class="p">)</span> <span class="p">{</span></span>
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3323
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<td class="diff-line-num new_line old" data-linenumber="3322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">VidSplitOk</span><span class="p">(</span><span class="n" style="color: #333;">orig_variant_id</span><span class="p">,</span> <span class="n" style="color: #333;">orig_allele_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3322
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<pre style="margin: 0;">+<span id="LC3322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_split</span><span class="p">)</span> <span class="p">{</span></span>
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3323
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<pre style="margin: 0;">+<span id="LC3323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">V<span class="idiff left right">ar</span>idSplitOk</span><span class="p">(</span><span class="n" style="color: #333;">orig_variant_id</span><span class="p">,</span> <span class="n" style="color: #333;">orig_allele_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3324
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3324
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<pre style="margin: 0;"> <span id="LC3324" class="line" lang="cpp"> <span class="n" style="color: #333;">varid_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">;</span></span>
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3325
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<pre style="margin: 0;">-<span id="LC3325" 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;">vid_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3325
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<pre style="margin: 0;">+<span id="LC3325" 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;">v<span class="idiff left right">ar</span>id_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3326
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3326
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<pre style="margin: 0;"> <span id="LC3326" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_orig_id</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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3327
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3327
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<pre style="margin: 0;"> <span id="LC3327" 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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3328
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3328
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<pre style="margin: 0;"> <span id="LC3328" class="line" lang="cpp"> <span class="n" style="color: #333;">varid_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3584" style="width: 35px; color: rgba(0,0,0,0.3); 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="3584" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3584,7 +3584,7 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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3584
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3584
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<pre style="margin: 0;"> <span id="LC3584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePvarSplit_ret_NOMEM</span><span class="p">;</span></span>
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3585
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3585
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<pre style="margin: 0;"> <span id="LC3585" class="line" lang="cpp"> <span class="p">}</span></span>
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3586
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3586
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<pre style="margin: 0;"> <span id="LC3586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_variant_id_overflow_missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfMiscNewVarIdOverflowMissing</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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3587
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<pre style="margin: 0;">-<span id="LC3587" 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;">v<span class="idiff left">id_dup</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2V</span>idDup</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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3587
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<pre style="margin: 0;">+<span id="LC3587" 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;">v<span class="idiff left">arid_dup</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2Var</span>idDup</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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3588
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3588
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<pre style="margin: 0;"> <span id="LC3588" class="line" lang="cpp"> <span class="n" style="color: #333;">VaridTemplate</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">varid_templatep</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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3589
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3589
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<pre style="margin: 0;"> <span id="LC3589" 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;">missing_varid_match</span><span class="p">)</span> <span class="p">{</span></span>
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3590
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3590
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<pre style="margin: 0;"> <span id="LC3590" class="line" lang="cpp"> <span class="n" style="color: #333;">missing_varid_match</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;">g_one_char_strs</span><span class="p">[</span><span class="mi" style="color: #099;">92</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// '.'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3600" style="width: 35px; color: rgba(0,0,0,0.3); 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="3600" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3600,7 +3600,7 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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3600
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3600
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<pre style="margin: 0;"> <span id="LC3600" class="line" lang="cpp"> <span class="p">}</span></span>
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3601
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3601
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<pre style="margin: 0;"> <span id="LC3601" 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;">overflow_substitute_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_variant_id_overflow_missing</span><span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">missing_varid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3602
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3602
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<pre style="margin: 0;"> <span id="LC3602" class="line" lang="cpp"> <span class="n" style="color: #333;">VaridTemplateInit</span><span class="p">(</span><span class="n" style="color: #333;">varid_template_str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_varid_match</span><span class="p">,</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">overflow_substitute_blen</span><span class="p">,</span> <span class="n" style="color: #333;">varid_templatep</span><span class="p">);</span></span>
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3603
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<pre style="margin: 0;">-<span id="LC3603" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3603
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<pre style="margin: 0;">+<span id="LC3603" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3604
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3604
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<pre style="margin: 0;"> <span id="LC3604" 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;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">insert_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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3605
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3605
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<pre style="margin: 0;"> <span id="LC3605" 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;">insert_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">insert_types</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">];</span></span>
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3606
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3606
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<pre style="margin: 0;"> <span id="LC3606" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">insert_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">insert_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">varid_templatep</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alleles_needed</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</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="3719" style="width: 35px; color: rgba(0,0,0,0.3); 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="3719" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3719,8 +3719,8 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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3719
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3719
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<pre style="margin: 0;"> <span id="LC3719" class="line" lang="cpp"></span>
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3720
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3720
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<pre style="margin: 0;"> <span id="LC3720" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VaridTemplate</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_varid_templatep</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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3721
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3721
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<pre style="margin: 0;"> <span id="LC3721" 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;">varid_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// for vid-split</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3722
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<pre style="margin: 0;">-<span id="LC3722" 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;">v<span class="idiff left">id_split</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2V</span>idSemicolon</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3723
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<td class="diff-line-num new_line old" data-linenumber="3722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3723" 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;">v<span class="idiff left">id_dup_nosplit</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">vid_dup</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="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">v</span>id_split</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3724" style="width: 35px; color: rgba(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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3722
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<pre style="margin: 0;">+<span id="LC3722" 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;">v<span class="idiff left">arid_split</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2Var</span>idSemicolon</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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3723
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<pre style="margin: 0;">+<span id="LC3723" 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;">v<span class="idiff left">arid_dup_nosplit</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">varid_dup</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="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">var</span>id_split</span><span class="p">);</span></span>
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3724
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3724
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<pre style="margin: 0;"> <span id="LC3724" 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;">split_just_snps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfMakePlink2MSplitBase</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kfMakePlink2MSplitSnps</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3725
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3725
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<pre style="margin: 0;"> <span id="LC3725" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">trs_variant_uidx</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="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3726
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3726
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<pre style="margin: 0;"> <span id="LC3726" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">variant_uidx_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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3766" style="width: 35px; color: rgba(0,0,0,0.3); 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="3766" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3766,16 +3766,16 @@ PglErr WritePvarSplit(const char* outname, const uintptr_t* variant_include, con</td>
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3766
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3766
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<pre style="margin: 0;"> <span id="LC3766" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">split_ct_p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_allele_ct</span><span class="p">;</span></span>
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3767
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<td class="diff-line-num new_line" data-linenumber="3767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3767
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<pre style="margin: 0;"> <span id="LC3767" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">keep_orig_id</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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3768
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3768
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<pre style="margin: 0;"> <span id="LC3768" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orig_allele_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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3769
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<td class="diff-line-num new_line old" data-linenumber="3769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3769" 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;">vid_dup_nosplit</span><span class="p">)</span> <span class="p">{</span></span>
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3769
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<pre style="margin: 0;">+<span id="LC3769" 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;">v<span class="idiff left right">ar</span>id_dup_nosplit</span><span class="p">)</span> <span class="p">{</span></span>
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3770
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3770
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<pre style="margin: 0;"> <span id="LC3770" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_orig_id</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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3771
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3771
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<pre style="margin: 0;"> <span id="LC3771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">varid_templatep</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;">missing_varid_match_blen</span><span class="p">))</span> <span class="p">{</span></span>
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3772
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3772
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<pre style="margin: 0;"> <span id="LC3772" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_varid_templatep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">varid_templatep</span><span class="p">;</span></span>
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3773
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<td class="diff-line-num new_line" data-linenumber="3773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3773
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<pre style="margin: 0;"> <span id="LC3773" 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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3774
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3774
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<pre style="margin: 0;"> <span id="LC3774" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_varid_templatep</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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3775
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<pre style="margin: 0;">-<span id="LC3775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vid_split</span><span class="p">)</span> <span class="p">{</span></span>
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3776
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<pre style="margin: 0;">-<span id="LC3776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">VidSplitOk</span><span class="p">(</span><span class="n" style="color: #333;">orig_variant_id</span><span class="p">,</span> <span class="n" style="color: #333;">orig_allele_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3775
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<pre style="margin: 0;">+<span id="LC3775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v<span class="idiff left right">ar</span>id_split</span><span class="p">)</span> <span class="p">{</span></span>
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3776
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<pre style="margin: 0;">+<span id="LC3776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">V<span class="idiff left right">ar</span>idSplitOk</span><span class="p">(</span><span class="n" style="color: #333;">orig_variant_id</span><span class="p">,</span> <span class="n" style="color: #333;">orig_allele_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3777
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3777
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<pre style="margin: 0;"> <span id="LC3777" class="line" lang="cpp"> <span class="n" style="color: #333;">varid_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_variant_id</span><span class="p">;</span></span>
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3778
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<pre style="margin: 0;">-<span id="LC3778" 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;">vid_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3778
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<pre style="margin: 0;">+<span id="LC3778" 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;">v<span class="idiff left right">ar</span>id_dup</span><span class="p">)</span> <span class="p">{</span></span>
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3779
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3779
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<pre style="margin: 0;"> <span id="LC3779" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_orig_id</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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3780
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3780
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<pre style="margin: 0;"> <span id="LC3780" 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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3781
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3781
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<pre style="margin: 0;"> <span id="LC3781" class="line" lang="cpp"> <span class="n" style="color: #333;">varid_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4230" style="width: 35px; color: rgba(0,0,0,0.3); 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="4230" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4230,7 +4230,7 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4230
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4230
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<pre style="margin: 0;"> <span id="LC4230" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_NOMEM;</span></span>
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4231
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4231
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<pre style="margin: 0;"> <span id="LC4231" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4232
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<td class="diff-line-num new_line" data-linenumber="4232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4232
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<pre style="margin: 0;"> <span id="LC4232" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t new_variant_id_overflow_missing = (misc_flags / kfMiscNewVarIdOverflowMissing) & 1;</span></span>
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4233
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<td class="diff-line-num new_line old" data-linenumber="4233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4233" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">id_dup = (make_plink2_flags / kfMakePlink2V</span>idDup) & 1;</span></span>
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4233
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<pre style="margin: 0;">+<span id="LC4233" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">arid_dup = (make_plink2_flags / kfMakePlink2Var</span>idDup) & 1;</span></span>
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4234
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4234
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<pre style="margin: 0;"> <span id="LC4234" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> VaridTemplate* varid_templatep = nullptr;</span></span>
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4235
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4235
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<pre style="margin: 0;"> <span id="LC4235" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!missing_varid_match) {</span></span>
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4236
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4236
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<pre style="margin: 0;"> <span id="LC4236" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> missing_varid_match = &(g_one_char_strs[92]); // '.'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4246,7 +4246,7 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4246
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4246
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<pre style="margin: 0;"> <span id="LC4246" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4247
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4247
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<pre style="margin: 0;"> <span id="LC4247" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t overflow_substitute_blen = new_variant_id_overflow_missing? (missing_varid_slen + 1) : 0;</span></span>
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4248
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4248
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<pre style="margin: 0;"> <span id="LC4248" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> VaridTemplateInit(varid_template_str, missing_varid_match, chr_buf, new_variant_id_max_allele_slen, overflow_substitute_blen, varid_templatep);</span></span>
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4249
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<pre style="margin: 0;">-<span id="LC4249" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (vid_dup) {</span></span>
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4249
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<pre style="margin: 0;">+<span id="LC4249" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (v<span class="idiff left right">ar</span>id_dup) {</span></span>
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4250
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4250
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<pre style="margin: 0;"> <span id="LC4250" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (uint32_t uii = 0; uii != varid_templatep->insert_ct; ++uii) {</span></span>
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4251
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4251
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<pre style="margin: 0;"> <span id="LC4251" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t insert_type = varid_templatep->insert_types[uii];</span></span>
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4252
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4252
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<pre style="margin: 0;"> <span id="LC4252" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((insert_type == 3) || ((insert_type == 2) && (varid_templatep->alleles_needed & 4))) {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4368,7 +4368,7 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4368
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4368
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<pre style="margin: 0;"> <span id="LC4368" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4369
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4369
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<pre style="margin: 0;"> <span id="LC4369" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> info_end_key_idx = IdHtableFind("END", info_keys, info_keys_htable, strlen("END"), info_keys_htable_size);</span></span>
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4370
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4370
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<pre style="margin: 0;"> <span id="LC4370" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (info_end_key_idx != UINT32_MAX) {</span></span>
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4371
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<pre style="margin: 0;">-<span id="LC4371" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const int32_t knum = const_container_of<span class="idiff left right">[</span>info_keys[info_end_key_idx], InfoVtype, key)->num;</span></span>
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4371
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<pre style="margin: 0;">+<span id="LC4371" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const int32_t knum = const_container_of<span class="idiff left right">(</span>info_keys[info_end_key_idx], InfoVtype, key)->num;</span></span>
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4372
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4372
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<pre style="margin: 0;"> <span id="LC4372" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((knum != 1) && (knum != kInfoVtypeUnknown)) {</span></span>
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4373
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4373
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<pre style="margin: 0;"> <span id="LC4373" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO: verify type instead.</span></span>
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4374
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4374
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<pre style="margin: 0;"> <span id="LC4374" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // but if number is not . or 1, this is not the INFO:END we're</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4407,8 +4407,8 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4407
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4407
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<pre style="margin: 0;"> <span id="LC4407" class="line" lang="cpp"></span>
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4408
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4408
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<pre style="margin: 0;"> <span id="LC4408" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const VaridTemplate* cur_varid_templatep = nullptr;</span></span>
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4409
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4409
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<pre style="margin: 0;"> <span id="LC4409" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* varid_token_start = nullptr; // for vid-split</span></span>
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4410
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<pre style="margin: 0;">-<span id="LC4410" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">id_split = (make_plink2_flags / kfMakePlink2V</span>idSemicolon) & 1;</span></span>
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4411
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<pre style="margin: 0;">-<span id="LC4411" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">id_dup_nosplit = vid_dup && (!v</span>id_split);</span></span>
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4410
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<pre style="margin: 0;">+<span id="LC4410" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">arid_split = (make_plink2_flags / kfMakePlink2Var</span>idSemicolon) & 1;</span></span>
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4411
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<pre style="margin: 0;">+<span id="LC4411" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t v<span class="idiff left right">arid_dup_nosplit = varid_dup && (!var</span>id_split);</span></span>
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4412
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4412
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<pre style="margin: 0;"> <span id="LC4412" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t next_variant_idx = 0;</span></span>
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4413
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4413
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<pre style="margin: 0;"> <span id="LC4413" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t trs_variant_uidx = 0;</span></span>
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4414
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4414
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<pre style="margin: 0;"> <span id="LC4414" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t next_variant_uidx = 0;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -4468,8 +4468,8 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4468
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4468
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<pre style="margin: 0;"> <span id="LC4468" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* const* cur_alleles = &(allele_storage[allele_idx_offset_base]);</span></span>
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4469
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4469
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<pre style="margin: 0;"> <span id="LC4469" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> JoinVtype jvt = JoinCount(cur_alleles, allele_ct, &next_jc);</span></span>
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4470
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4470
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<pre style="margin: 0;"> <span id="LC4470" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // previously validated</span></span>
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4471
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<pre style="margin: 0;">-<span id="LC4471" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">if ((join_mode == kfMakePlink2MJoinSnps) && </span>) {</span></span>
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4472
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<pre style="margin: 0;">-<span id="LC4472" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4471
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<pre style="margin: 0;">+<span id="LC4471" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">// if ((join_mode == kfMakePlink2MJoinSnps) && ()</span>) {</span></span>
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4472
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<pre style="margin: 0;">+<span id="LC4472" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">// </span>}</span></span>
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4473
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4473
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<pre style="margin: 0;"> <span id="LC4473" class="line" lang="cpp"></span>
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4474
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4474
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<pre style="margin: 0;"> <span id="LC4474" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO</span></span>
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4475
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4475
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<pre style="margin: 0;"> <span id="LC4475" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc.snp_ct += next_jc.snp_ct;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -4482,75 +4482,56 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4482
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4482
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<pre style="margin: 0;"> <span id="LC4482" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // No join needed. This is usually the common case, so we duplicate a</span></span>
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4483
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4483
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<pre style="margin: 0;"> <span id="LC4483" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // bunch of code for the sake of avoiding slowdown here.</span></span>
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4484
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4484
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<pre style="margin: 0;"> <span id="LC4484" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = memcpya(cswritep, chr_buf, chr_buf_blen);</span></span>
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4485
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<pre style="margin: 0;">-<span id="LC4485" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = u32toa_x(variant_bps[variant_uidx], '\t', cswritep);</span></span>
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4486
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<pre style="margin: 0;">-<span id="LC4486" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpyax(cswritep, variant_ids[variant_uidx], '\t');</span></span>
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<pre style="margin: 0;">+<span id="LC4485" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = u32toa_x(variant_bps[<span class="idiff left right">bp_start_</span>variant_uidx], '\t', cswritep);</span></span>
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<pre style="margin: 0;">+<span id="LC4486" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpyax(cswritep, variant_ids[<span class="idiff left right">bp_start_</span>variant_uidx], '\t');</span></span>
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4487
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<pre style="margin: 0;"> <span id="LC4487" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uintptr_t allele_idx_offset_base;</span></span>
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4488
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4488
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<pre style="margin: 0;"> <span id="LC4488" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!allele_idx_offsets) {</span></span>
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4489
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<pre style="margin: 0;">-<span id="LC4489" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> allele_idx_offset_base = variant_uidx * 2;</span></span>
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4489
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<pre style="margin: 0;">+<span id="LC4489" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> allele_idx_offset_base = <span class="idiff left right">bp_start_</span>variant_uidx * 2;</span></span>
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4490
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4490
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<pre style="margin: 0;"> <span id="LC4490" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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4491
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<pre style="margin: 0;">-<span id="LC4491" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> allele_idx_offset_base = allele_idx_offsets[variant_uidx];</span></span>
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4492
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<pre style="margin: 0;">-<span id="LC4492" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">cur_allele_ct = allele_idx_offsets[</span>variant_uidx + 1] - allele_idx_offset_base;</span></span>
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4491
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<pre style="margin: 0;">+<span id="LC4491" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> allele_idx_offset_base = allele_idx_offsets[<span class="idiff left right">bp_start_</span>variant_uidx];</span></span>
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4492
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<pre style="margin: 0;">+<span id="LC4492" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right">allele_ct = allele_idx_offsets[bp_start_</span>variant_uidx + 1] - allele_idx_offset_base;</span></span>
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4493
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4493
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<pre style="margin: 0;"> <span id="LC4493" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4494
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4494
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<pre style="margin: 0;"> <span id="LC4494" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* const* cur_alleles = &(allele_storage[allele_idx_offset_base]);</span></span>
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4495
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<pre style="margin: 0;">-<span id="LC4495" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (refalt1_select) {</span></span>
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4496
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<pre style="margin: 0;">-<span id="LC4496" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ref_allele_idx = refalt1_select[variant_uidx][0];</span></span>
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4497
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<td class="diff-line-num new_line old" data-linenumber="4495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4497" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> alt1_allele_idx = refalt1_select[variant_uidx][1];</span></span>
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4498
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<pre style="margin: 0;">-<span id="LC4498" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4499
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<pre style="margin: 0;">-<span id="LC4499" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpyax(cswritep, cur_alleles[ref_allele_idx], '\t');</span></span>
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4500
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<pre style="margin: 0;">-<span id="LC4500" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t alt_allele_written = 0;</span></span>
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4501
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<pre style="margin: 0;">-<span id="LC4501" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((!allele_presents) || IsSet(allele_presents, allele_idx_offset_base + alt1_allele_idx)) {</span></span>
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4502
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<td class="diff-line-num new_line old" data-linenumber="4495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4502" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, cur_alleles[alt1_allele_idx]);</span></span>
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4503
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<td class="diff-line-num new_line old" data-linenumber="4495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4503" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> alt_allele_written = 1;</span></span>
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4504
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<pre style="margin: 0;">-<span id="LC4504" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4495
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<pre style="margin: 0;">+<span id="LC4495" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpyax(cswritep, cur_alleles[0], '\t');</span></span>
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4496
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<pre style="margin: 0;">+<span id="LC4496" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, cur_alleles[1]);</span></span>
</pre>
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4505
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4497
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<pre style="margin: 0;"> <span id="LC4497" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(Cswrite(&css, &cswritep))) {</span></span>
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4506
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<pre style="margin: 0;">-<span id="LC4506" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvar_ret_WRITE_FAIL;</span></span>
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4498
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<pre style="margin: 0;">+<span id="LC4498" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvar<span class="idiff left right">Join</span>_ret_WRITE_FAIL;</span></span>
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4507
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4499
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<pre style="margin: 0;"> <span id="LC4499" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4508
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<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4508" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (cur_allele_ct > 2) {</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4509
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4509" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (uint32_t allele_idx = 0; allele_idx != cur_allele_ct; ++allele_idx) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4510
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<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4510" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((allele_idx == ref_allele_idx) || (allele_idx == alt1_allele_idx) || (allele_presents && (!IsSet(allele_presents, allele_idx_offset_base + allele_idx)))) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4511
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<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4511" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> continue;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4512
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4512" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4513
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4513" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (alt_allele_written) {</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4514
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4514" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = ',';</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4515
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4515" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4516
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<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4516" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> alt_allele_written = 1;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4517
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4517" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, cur_alleles[allele_idx]);</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4518
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4518" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(Cswrite(&css, &cswritep))) {</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4519
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4519" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvar_ret_WRITE_FAIL;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4520
</td>
<td class="diff-line-num new_line old" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4520" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4500
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4500" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (uint32_t allele_idx = 2; allele_idx != allele_ct; ++allele_idx) {</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4501
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4501" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = ',';</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4502
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4502" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, cur_alleles[allele_idx]);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4503
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4503" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(Cswrite(&css, &cswritep))) {</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4504
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4504" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_WRITE_FAIL;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4521
</td>
<td class="diff-line-num new_line" data-linenumber="4505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4505
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4505" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4522
</td>
<td class="diff-line-num new_line" data-linenumber="4506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4506
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4506" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4523
</td>
<td class="diff-line-num new_line old" data-linenumber="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4523" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!alt_allele_written) {</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4524
</td>
<td class="diff-line-num new_line old" data-linenumber="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4524" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = output_missing_geno_char;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4525
</td>
<td class="diff-line-num new_line old" data-linenumber="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4525" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4526
</td>
<td class="diff-line-num new_line" data-linenumber="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4507
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4507" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4527
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<td class="diff-line-num new_line" data-linenumber="4508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4508
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<pre style="margin: 0;"> <span id="LC4508" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_qual) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4528
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<td class="diff-line-num new_line" data-linenumber="4509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4509
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<pre style="margin: 0;"> <span id="LC4509" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '\t';</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4529
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<td class="diff-line-num new_line old" data-linenumber="4510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4529" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((!qual_present) || (!IsSet(qual_present, variant_uidx))) {</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4530" style="width: 35px; color: rgba(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="4510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4510
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<pre style="margin: 0;">+<span id="LC4510" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((!qual_present) || (!IsSet(qual_present, <span class="idiff left right">bp_start_</span>variant_uidx))) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4530
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<td class="diff-line-num new_line" data-linenumber="4511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4511
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<pre style="margin: 0;"> <span id="LC4511" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '.';</span></span>
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<td class="diff-line-num old_line" data-linenumber="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4531
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<td class="diff-line-num new_line" data-linenumber="4512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4512
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4512" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4532
</td>
<td class="diff-line-num new_line old" data-linenumber="4513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4532" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = ftoa_g(quals[variant_uidx], cswritep);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4533" style="width: 35px; color: rgba(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="4513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4513
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<pre style="margin: 0;">+<span id="LC4513" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = ftoa_g(quals[<span class="idiff left right">bp_start_</span>variant_uidx], cswritep);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4533
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<td class="diff-line-num new_line" data-linenumber="4514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4514
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<pre style="margin: 0;"> <span id="LC4514" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4534
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<td class="diff-line-num new_line" data-linenumber="4515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4515
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<pre style="margin: 0;"> <span id="LC4515" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4535
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<td class="diff-line-num new_line" data-linenumber="4516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4516
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<pre style="margin: 0;"> <span id="LC4516" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4536
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<td class="diff-line-num new_line" data-linenumber="4517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4517
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4517" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_filter) {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4537
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<td class="diff-line-num new_line" data-linenumber="4518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4518
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<pre style="margin: 0;"> <span id="LC4518" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '\t';</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4538
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<td class="diff-line-num new_line old" data-linenumber="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4538" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((!filter_present) || (!IsSet(filter_present, variant_uidx))) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4539" style="width: 35px; color: rgba(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="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4519
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<pre style="margin: 0;">+<span id="LC4519" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((!filter_present) || (!IsSet(filter_present, <span class="idiff left right">bp_start_</span>variant_uidx))) {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4539
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<td class="diff-line-num new_line" data-linenumber="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4520
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<pre style="margin: 0;"> <span id="LC4520" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '.';</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4540
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<td class="diff-line-num new_line old" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4540" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else if (!IsSet(filter_npass, variant_uidx)) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4521
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<pre style="margin: 0;">+<span id="LC4521" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else if (!IsSet(filter_npass, <span class="idiff left right">bp_start_</span>variant_uidx)) {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4541
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<td class="diff-line-num new_line" data-linenumber="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4522
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<pre style="margin: 0;"> <span id="LC4522" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya_k(cswritep, "PASS");</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4542
</td>
<td class="diff-line-num new_line" data-linenumber="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4523
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<pre style="margin: 0;"> <span id="LC4523" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4543
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<td class="diff-line-num new_line old" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4543" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, filter_storage[variant_uidx]);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4524
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<pre style="margin: 0;">+<span id="LC4524" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = strcpya(cswritep, filter_storage[<span class="idiff left right">bp_start_</span>variant_uidx]);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4544
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<td class="diff-line-num new_line" data-linenumber="4525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4525" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4545
</td>
<td class="diff-line-num new_line" data-linenumber="4526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4526
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<pre style="margin: 0;"> <span id="LC4526" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4546
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<td class="diff-line-num new_line" data-linenumber="4527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4527
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<pre style="margin: 0;"> <span id="LC4527" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4547
</td>
<td class="diff-line-num new_line" data-linenumber="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4528
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4528" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (write_info) {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4548
</td>
<td class="diff-line-num new_line" data-linenumber="4529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4529
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4529" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '\t';</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4549
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<td class="diff-line-num new_line old" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4549" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t is_pr = all_nonref || (nonref_flags && IsSet(nonref_flags, variant_uidx));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4550" style="width: 35px; color: rgba(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="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4530
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<pre style="margin: 0;">+<span id="LC4530" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t is_pr = all_nonref || (nonref_flags && IsSet(nonref_flags, <span class="idiff left right">bp_start_</span>variant_uidx));</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4550
</td>
<td class="diff-line-num new_line" data-linenumber="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4531
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4531" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pvar_info_line_iter) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4551
</td>
<td class="diff-line-num new_line old" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4551" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = PvarInfoReloadAndWrite(info_pr_flag_present, info_col_idx, variant_uidx, is_pr, &pvar_reload_txs, &pvar_info_line_iter, &cswritep, &trs_variant_uidx);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4532
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4532" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = PvarInfoReloadAndWrite(info_pr_flag_present, info_col_idx, <span class="idiff left right">bp_start_</span>variant_uidx, is_pr, &pvar_reload_txs, &pvar_info_line_iter, &cswritep, &trs_variant_uidx);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4552
</td>
<td class="diff-line-num new_line" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4533
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4533" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(reterr)) {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4553
</td>
<td class="diff-line-num new_line old" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4553" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvar_ret_TSTREAM_FAIL;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4534
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<pre style="margin: 0;">+<span id="LC4534" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvar<span class="idiff left right">Join</span>_ret_TSTREAM_FAIL;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4554
</td>
<td class="diff-line-num new_line" data-linenumber="4535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4535
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4535" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4555
</td>
<td class="diff-line-num new_line" data-linenumber="4536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4536
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4536" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4556
</td>
<td class="diff-line-num new_line" data-linenumber="4537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4537
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4537" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (is_pr) {</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4566" style="width: 35px; color: rgba(0,0,0,0.3); 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="4547" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4566,50 +4547,26 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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<td class="diff-line-num old_line" data-linenumber="4566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4566
</td>
<td class="diff-line-num new_line" data-linenumber="4547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4547
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4547" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!variant_cms) {</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4567
</td>
<td class="diff-line-num new_line" data-linenumber="4548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4548
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4548" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *cswritep++ = '0';</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4568
</td>
<td class="diff-line-num new_line" data-linenumber="4549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4549
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4549" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4569
</td>
<td class="diff-line-num new_line old" data-linenumber="4550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC4569" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = dtoa_g_p8(variant_cms[variant_uidx], cswritep);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4550
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4550" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cswritep = dtoa_g_p8(variant_cms[<span class="idiff left right">bp_start_</span>variant_uidx], cswritep);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4570
</td>
<td class="diff-line-num new_line" data-linenumber="4551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4551
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4551" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4571
</td>
<td class="diff-line-num new_line" data-linenumber="4552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4552
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4552" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4572
</td>
<td class="diff-line-num new_line" data-linenumber="4553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4553
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4553" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> AppendBinaryEoln(&cswritep);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4573
</td>
<td class="diff-line-num new_line old" data-linenumber="4554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4573" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
</pre>
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4554
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<pre style="margin: 0;">+<span id="LC4554" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // next_jc guaranteed to be zero-initialized</span></span>
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4555
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<pre style="margin: 0;">+<span id="LC4555" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else if (next_variant_idx) {</span></span>
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4574
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4556
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<pre style="margin: 0;"> <span id="LC4556" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // TODO</span></span>
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4575
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<pre style="margin: 0;">-<span id="LC4575" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.snp_ct = 0;</span></span>
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4576
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4576" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.nonsnp_ct = 0;</span></span>
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4577
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<pre style="margin: 0;">-<span id="LC4577" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.symbolic_ct = 0;</span></span>
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4578
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4578" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_snp_ct = 0;</span></span>
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4579
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4579" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_nonsnp_ct = 0;</span></span>
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4580
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<pre style="margin: 0;">-<span id="LC4580" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4581
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<pre style="margin: 0;">-<span id="LC4581" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (next_variant_idx == variant_ct) {</span></span>
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4582
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4582" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
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4583
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<pre style="margin: 0;">-<span id="LC4583" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4584
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<pre style="margin: 0;">-<span id="LC4584" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> this_pos_write_variant_ct = 0;</span></span>
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4585
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<pre style="margin: 0;">-<span id="LC4585" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc = next_jc;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4586
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4586" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> prev_bp = cur_bp;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4587
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4587" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_idx = next_variant_idx;</span></span>
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4588
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4588" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_uidx = next_variant_uidx;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4589
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4589" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (next_variant_idx >= next_print_variant_idx) {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4590
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4590" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pct > 10) {</span></span>
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4591
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4591" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> putc_unlocked('\b', stdout);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4592
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4592" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4593
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4593" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> pct = (next_variant_idx * 100LLU) / variant_ct;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4594
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4594" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf("\b\b%u%%", pct++);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4595
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4595" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fflush(stdout);</span></span>
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4596
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<pre style="margin: 0;">-<span id="LC4596" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_print_variant_idx = (pct * S_CAST(uint64_t, variant_ct)) / 100;</span></span>
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4597
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4597" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4598
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<td class="diff-line-num new_line old" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4598" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ;;;</span></span>
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4599
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<pre style="margin: 0;">-<span id="LC4599" class="line" lang="cpp"></span>
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4600
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<pre style="margin: 0;">-<span id="LC4600" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="4601" style="width: 35px; color: rgba(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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4557
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<pre style="margin: 0;">+<span id="LC4557" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ;;;;</span></span>
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4601
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<td class="diff-line-num new_line" data-linenumber="4558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4558
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<pre style="margin: 0;"> <span id="LC4558" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* orig_variant_id = variant_ids[variant_uidx];</span></span>
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<td class="diff-line-num old_line" data-linenumber="4602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4602
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<td class="diff-line-num new_line" data-linenumber="4559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4559
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<pre style="margin: 0;"> <span id="LC4559" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* ref_allele = cur_alleles[0];</span></span>
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4603
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<td class="diff-line-num new_line" data-linenumber="4560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4560
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<pre style="margin: 0;"> <span id="LC4560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const uint32_t ref_allele_slen = strlen(ref_allele);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4604
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<td class="diff-line-num new_line" data-linenumber="4561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4561
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<pre style="margin: 0;"> <span id="LC4561" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> uint32_t split_ct_p1 = allele_ct;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4605
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<td class="diff-line-num new_line" data-linenumber="4562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4562
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<pre style="margin: 0;"> <span id="LC4562" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (allele_ct > 2) {</span></span>
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4606
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<td class="diff-line-num new_line old" data-linenumber="4563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4606" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!vid_dup) {</span></span>
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4563
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<pre style="margin: 0;">+<span id="LC4563" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (!v<span class="idiff left right">ar</span>id_dup) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4607
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<td class="diff-line-num new_line" data-linenumber="4564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4564
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<pre style="margin: 0;"> <span id="LC4564" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (varid_templatep && (!missing_varid_match_blen)) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4608
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<td class="diff-line-num new_line" data-linenumber="4565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4565
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<pre style="margin: 0;"> <span id="LC4565" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cur_varid_templatep = varid_templatep;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4609
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<td class="diff-line-num new_line" data-linenumber="4566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4566
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<pre style="margin: 0;"> <span id="LC4566" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4610
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<td class="diff-line-num new_line" data-linenumber="4567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4567
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<pre style="margin: 0;"> <span id="LC4567" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> cur_varid_templatep = nullptr;</span></span>
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4611
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<td class="diff-line-num new_line old" data-linenumber="4568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4611" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (vid_split) {</span></span>
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4612
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<td class="diff-line-num new_line old" data-linenumber="4568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4612" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (VidSplitOk(orig_variant_id, allele_ct)) {</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4613" style="width: 35px; color: rgba(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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4568
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<pre style="margin: 0;">+<span id="LC4568" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (v<span class="idiff left right">ar</span>id_split) {</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4613" style="width: 35px; color: rgba(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="4569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4569
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<pre style="margin: 0;">+<span id="LC4569" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (V<span class="idiff left right">ar</span>idSplitOk(orig_variant_id, allele_ct)) {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4613
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<td class="diff-line-num new_line" data-linenumber="4570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4570
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<pre style="margin: 0;"> <span id="LC4570" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> varid_token_start = orig_variant_id;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4614
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<td class="diff-line-num new_line" data-linenumber="4571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4571
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<pre style="margin: 0;"> <span id="LC4571" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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<td class="diff-line-num old_line" data-linenumber="4615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4615
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4572
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<pre style="margin: 0;"> <span id="LC4572" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> varid_token_start = nullptr;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4624" style="width: 35px; color: rgba(0,0,0,0.3); 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="4581" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4624,6 +4581,30 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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4624
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4581
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<pre style="margin: 0;"> <span id="LC4581" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4625
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4582
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<pre style="margin: 0;"> <span id="LC4582" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4626
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4583
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<pre style="margin: 0;"> <span id="LC4583" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4584
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<pre style="margin: 0;">+<span id="LC4584" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ;;;;</span></span>
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4585
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<pre style="margin: 0;">+<span id="LC4585" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.snp_ct = 0;</span></span>
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4586
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<pre style="margin: 0;">+<span id="LC4586" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.nonsnp_ct = 0;</span></span>
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4587
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<pre style="margin: 0;">+<span id="LC4587" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.symbolic_ct = 0;</span></span>
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4588
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<pre style="margin: 0;">+<span id="LC4588" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_snp_ct = 0;</span></span>
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4589
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<pre style="margin: 0;">+<span id="LC4589" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_jc.missalt_nonsnp_ct = 0;</span></span>
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4590
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<pre style="margin: 0;">+<span id="LC4590" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4591
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<pre style="margin: 0;">+<span id="LC4591" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (next_variant_idx == variant_ct) {</span></span>
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4592
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<pre style="margin: 0;">+<span id="LC4592" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
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4593
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<pre style="margin: 0;">+<span id="LC4593" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4594
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<pre style="margin: 0;">+<span id="LC4594" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> // this_pos_write_variant_ct = 0;</span></span>
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4595
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<pre style="margin: 0;">+<span id="LC4595" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> jc = next_jc;</span></span>
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4596
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<pre style="margin: 0;">+<span id="LC4596" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> prev_bp = cur_bp;</span></span>
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4597
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<pre style="margin: 0;">+<span id="LC4597" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_idx = next_variant_idx;</span></span>
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4598
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<pre style="margin: 0;">+<span id="LC4598" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bp_start_variant_uidx = next_variant_uidx;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4599
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<pre style="margin: 0;">+<span id="LC4599" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (next_variant_idx >= next_print_variant_idx) {</span></span>
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4600
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<pre style="margin: 0;">+<span id="LC4600" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (pct > 10) {</span></span>
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4601
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<pre style="margin: 0;">+<span id="LC4601" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> putc_unlocked('\b', stdout);</span></span>
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4602
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<pre style="margin: 0;">+<span id="LC4602" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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4603
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<pre style="margin: 0;">+<span id="LC4603" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> pct = (next_variant_idx * 100LLU) / variant_ct;</span></span>
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4604
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<pre style="margin: 0;">+<span id="LC4604" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf("\b\b%u%%", pct++);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4627" style="width: 35px; color: rgba(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="4605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4605
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4605" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fflush(stdout);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4606
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4606" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> next_print_variant_idx = (pct * S_CAST(uint64_t, variant_ct)) / 100;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4627" style="width: 35px; color: rgba(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="4607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4607
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4607" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4627
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<td class="diff-line-num new_line" data-linenumber="4608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4608
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4608" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4628
</td>
<td class="diff-line-num new_line" data-linenumber="4609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4609
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (unlikely(CswriteCloseNull(&css, cswritep))) {</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4629
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<td class="diff-line-num new_line" data-linenumber="4610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4610
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4610" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> goto WritePvarJoin_ret_WRITE_FAIL;</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4638" style="width: 35px; color: rgba(0,0,0,0.3); 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="4619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4638,7 +4619,7 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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<td class="diff-line-num old_line" data-linenumber="4638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4638
</td>
<td class="diff-line-num new_line" data-linenumber="4619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4619
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4619" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = kPglRetNomem;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4639
</td>
<td class="diff-line-num new_line" data-linenumber="4620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4620
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4620" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4640
</td>
<td class="diff-line-num new_line" data-linenumber="4621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4621
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4621" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WritePvarJoin_ret_TSTREAM_FAIL:</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4641
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<td class="diff-line-num new_line old" data-linenumber="4622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4641" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> TextStreamErrPrint(pvar_info_reload, &pvar_reload_txs<span class="idiff left right">, &reterr</span>);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4622
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<pre style="margin: 0;">+<span id="LC4622" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> TextStreamErrPrint(pvar_info_reload, &pvar_reload_txs);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4642
</td>
<td class="diff-line-num new_line" data-linenumber="4623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4623
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<pre style="margin: 0;"> <span id="LC4623" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4643
</td>
<td class="diff-line-num new_line" data-linenumber="4624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4624
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4624" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WritePvarJoin_ret_WRITE_FAIL:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4644
</td>
<td class="diff-line-num new_line" data-linenumber="4625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4625
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4625" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = kPglRetWriteFail;</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4646" style="width: 35px; color: rgba(0,0,0,0.3); 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="4627" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4646,6 +4627,9 @@ PglErr WritePvarJoin(const char* outname, const uintptr_t* variant_include, cons</td>
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<td class="diff-line-num old_line" data-linenumber="4646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4646
</td>
<td class="diff-line-num new_line" data-linenumber="4627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4627
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4627" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WritePvarJoin_ret_INVALID_CMDLINE:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4647
</td>
<td class="diff-line-num new_line" data-linenumber="4628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4628
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4628" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = kPglRetInvalidCmdline;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4648
</td>
<td class="diff-line-num new_line" data-linenumber="4629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4629
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4629" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="4649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4630
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<pre style="margin: 0;">+<span id="LC4630" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WritePvarJoin_ret_INCONSISTENT_INPUT:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4631
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4631" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> reterr = kPglRetInconsistentInput;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="4632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4632
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4632" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> break;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4649
</td>
<td class="diff-line-num new_line" data-linenumber="4633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4633
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4633" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4650
</td>
<td class="diff-line-num new_line" data-linenumber="4634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4634
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4634" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> WritePvarJoin_ret_1:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4651
</td>
<td class="diff-line-num new_line" data-linenumber="4635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4635
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<pre style="margin: 0;"> <span id="LC4635" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> CswriteCloseCond(&css, cswritep);</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="6673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6689,6 +6673,7 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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6689
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6673
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<pre style="margin: 0;"> <span id="LC6673" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_write_allele_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_allele_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6690
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<td class="diff-line-num new_line" data-linenumber="6674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6674
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<pre style="margin: 0;"> <span id="LC6674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_missalt_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="6691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6691
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<td class="diff-line-num new_line" data-linenumber="6675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6675
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<pre style="margin: 0;"> <span id="LC6675" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MMask</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6692" style="width: 35px; color: rgba(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="6676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6676
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<pre style="margin: 0;">+<span id="LC6676" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: enforce on command line</span></span>
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6692
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6677
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<pre style="margin: 0;"> <span id="LC6677" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">refalt1_select</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;">allele_presents</span><span class="p">));</span></span>
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6693
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6678
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<pre style="margin: 0;"> <span id="LC6678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMakePlink2MJoin</span><span class="p">)</span> <span class="p">{</span></span>
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6694
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6679
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<pre style="margin: 0;"> <span id="LC6679" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PlanMultiallelicJoin</span><span class="p">(</span><span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">make_plink2_flags</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">write_variant_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">write_allele_idx_offsets</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_write_allele_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">max_missalt_ct</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6736" style="width: 35px; color: rgba(0,0,0,0.3); 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="6721" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6736,7 +6721,7 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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6736
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<td class="diff-line-num new_line" data-linenumber="6721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6721
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<pre style="margin: 0;"> <span id="LC6721" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WriteMapOrBim</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">allele_presents</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">,</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">,</span> <span class="n" style="color: #333;">bim_zst</span><span class="p">,</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6737
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6722
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<pre style="margin: 0;"> <span id="LC6722" 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="6738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6738
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<td class="diff-line-num new_line" data-linenumber="6723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6723
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<pre style="margin: 0;"> <span id="LC6723" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">write_variant_ct</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variant_ct</span><span class="p">);</span></span>
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6739
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<td class="diff-line-num new_line old" data-linenumber="6724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6739" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WriteBimSplit</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="n" style="color: #333;">varid_template_str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_varid_match</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">idSemicolon</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2V</span>idDup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">bim_zst</span><span class="p">,</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6724
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<pre style="margin: 0;">+<span id="LC6724" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WriteBimSplit</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="n" style="color: #333;">varid_template_str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_varid_match</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="n" style="color: #333;">new_variant_id_max_allele_slen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">make_plink2_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left">aridSemicolon</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">make_plink2_flags</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kfMakePlink2Var</span>idDup</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">bim_zst</span><span class="p">,</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">);</span></span>
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6740
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6725
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<pre style="margin: 0;"> <span id="LC6725" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC6726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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6742
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6727
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<pre style="margin: 0;"> <span id="LC6727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_ret_1</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/394d8a281efdc53907dca6c9cc8dbb8c15317766#a125279a9188813c60a6fe3d56cead0bd36fcc8f"><strong>plink2_data.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,8 +45,8 @@ FLAGSET_DEF_START()</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2TrimAlts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">10</span><span class="p">),</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2MMask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kfMakePlink2TrimAlts</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfMakePlink2MSplitBase</span><span class="p">,</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2EraseAlt2Plus</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">11</span><span class="p">),</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2VidSemicolon</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">12</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2VidDup</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">13</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idSemicolon</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">12</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2V<span class="idiff left right">ar</span>idDup</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">13</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2SetHhMissing</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">14</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">kfMakePlink2SetHhMissingKeepDosage</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">15</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/394d8a281efdc53907dca6c9cc8dbb8c15317766#82c8c0946825d16815c68e845955a90079d70b6b"><strong>plink2_glm.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">@@ -1160,6 +1160,8 @@ ENUM_U31_DEF_START()</td>
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1160
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="cpp"> <span class="n" style="color: #333;">kGlmErrcodeLogisticConvergeFail</span><span class="p">,</span></span>
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1161
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1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="cpp"> <span class="n" style="color: #333;">kGlmErrcodeFirthConvergeFail</span><span class="p">,</span></span>
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1162
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1162
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="cpp"> <span class="n" style="color: #333;">kGlmErrcodeInvalidResult</span><span class="p">,</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// no codes for logistic-unfinished and firth-unfinished for now since we</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// still report results there</span></span>
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1163
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="cpp"></span>
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1164
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// only during initial scan</span></span>
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1165
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="cpp"> <span class="n" style="color: #333;">kGlmErrcodeUnstableScale</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">@@ -2721,7 +2723,7 @@ void SolveLinearSystem(const float* ll, const float* yy, uint32_t predictor_ct,</td>
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2721
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2723
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<pre style="margin: 0;"> <span id="LC2723" class="line" lang="cpp"> <span class="p">}</span></span>
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2724
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<pre style="margin: 0;"> <span id="LC2724" class="line" lang="cpp"><span class="p">}</span></span>
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2725
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<pre style="margin: 0;"> <span id="LC2725" class="line" lang="cpp"></span>
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2724
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<pre style="margin: 0;">-<span id="LC2724" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">LogisticRegression</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yy</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ll</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grad</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dcoef</span><span class="p">)</span> <span class="p">{</span></span>
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2726
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<pre style="margin: 0;">+<span id="LC2726" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">LogisticRegression</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yy</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_unfinished_ptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ll</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grad</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dcoef</span><span class="p">)</span> <span class="p">{</span></span>
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2725
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2727
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<pre style="margin: 0;"> <span id="LC2727" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Similar to first part of logistic.cpp fitLM(), but incorporates changes</span></span>
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2726
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2728
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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// from Pascal Pons et al.'s TopCoder code.</span></span>
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2727
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2729
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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2813" style="width: 35px; color: rgba(0,0,0,0.3); 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="2815" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2813,6 +2815,7 @@ BoolErr LogisticRegression(const float* yy, const float* xx, uint32_t sample_ct,</td>
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2813
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2815
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<pre style="margin: 0;"> <span id="LC2815" 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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2814
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2816
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<pre style="margin: 0;"> <span id="LC2816" class="line" lang="cpp"> <span class="p">}</span></span>
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2815
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2817
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<pre style="margin: 0;"> <span id="LC2817" class="line" lang="cpp"> <span class="p">}</span></span>
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2818
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<pre style="margin: 0;">+<span id="LC2818" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">is_unfinished_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2816
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2819
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<pre style="margin: 0;"> <span id="LC2819" 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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2817
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2820
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<pre style="margin: 0;"> <span id="LC2820" class="line" lang="cpp"> <span class="p">}</span></span>
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2821
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<pre style="margin: 0;"> <span id="LC2821" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); 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="2877" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2874,7 +2877,7 @@ void FirthComputeWeights(const float* yy, const float* xx, const float* pp, cons</td>
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2874
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2877
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC2879" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2877" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">FirthRegression</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yy</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">half_inverted_buf</span><span class="p">,</span> <span class="n" style="color: #333;">MatrixInvertBuf1</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inv_1d_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dbl_2d_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grad</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dcoef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ww</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmpnxk_buf</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2880" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">FirthRegression</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">yy</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">is_unfinished_ptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">half_inverted_buf</span><span class="p">,</span> <span class="n" style="color: #333;">MatrixInvertBuf1</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">inv_1d_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dbl_2d_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">grad</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dcoef</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ww</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmpnxk_buf</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2881" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This is a port of Georg Heinze's logistf R function, adapted to use many</span></span>
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2882
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<pre style="margin: 0;"> <span id="LC2882" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of plink 1.9's optimizations; see</span></span>
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<pre style="margin: 0;"> <span id="LC2883" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// http://cemsiis.meduniwien.ac.at/en/kb/science-research/software/statistical-software/fllogistf/</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">@@ -2902,6 +2905,8 @@ BoolErr FirthRegression(const float* yy, const float* xx, uint32_t sample_ct, ui</td>
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2902
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2905
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<pre style="margin: 0;"> <span id="LC2905" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// too)</span></span>
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2903
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2906
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<pre style="margin: 0;"> <span id="LC2906" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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2907
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<pre style="margin: 0;"> <span id="LC2907" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Returns 0 on success, 1 on convergence failure.</span></span>
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<pre style="margin: 0;">+<span id="LC2908" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// is_unfinished assumed to be initialized to 0, and is set to 1 if we hit</span></span>
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<pre style="margin: 0;">+<span id="LC2909" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the iteration limit without satisfying other convergence criteria.</span></span>
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2910
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<pre style="margin: 0;"> <span id="LC2910" 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;">predictor_ctav</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kFloatPerFVec</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2911" 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_ctav</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">kFloatPerFVec</span><span class="p">);</span></span>
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2912
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<pre style="margin: 0;"> <span id="LC2912" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">is_last_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2934,15 +2939,18 @@ BoolErr FirthRegression(const float* yy, const float* xx, uint32_t sample_ct, ui</td>
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<pre style="margin: 0;"> <span id="LC2939" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (4 Nov 2017): grad[] trailing elements must be zeroed out</span></span>
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2940
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<pre style="margin: 0;"> <span id="LC2940" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroFArr</span><span class="p">(</span><span class="n" style="color: #333;">predictor_ctav</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">predictor_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">grad</span><span class="p">[</span><span class="n" style="color: #333;">predictor_ct</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC2941" class="line" lang="cpp"></span>
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2937
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<pre style="margin: 0;">-<span id="LC2937" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// start with 80% of logistf convergence defaults (some reduction is</span></span>
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2938
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<pre style="margin: 0;">-<span id="LC2938" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// appropriate to be consistent with single-precision arithmetic); may tune</span></span>
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<pre style="margin: 0;">-<span id="LC2939" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// later.</span></span>
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<pre style="margin: 0;">+<span id="LC2942" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// start with 80% of most logistf convergence defaults (some reduction is</span></span>
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<pre style="margin: 0;">+<span id="LC2943" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// appropriate to be consistent with single-precision arithmetic). (Update,</span></span>
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<pre style="margin: 0;">+<span id="LC2944" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 9 Apr 2020: max_iter now matches logistf default since we've been shown a</span></span>
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<pre style="margin: 0;">+<span id="LC2945" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// concrete example where it matters in a way that isn't masked by the</span></span>
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<pre style="margin: 0;">+<span id="LC2946" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// single- vs. double-precision difference.)</span></span>
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<pre style="margin: 0;">+<span id="LC2947" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC2948" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// see also the hs_bail condition: if we ever try all five halfsteps, when</span></span>
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<pre style="margin: 0;"> <span id="LC2949" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// dcoef_max and grad_max aren't that far from the normal convergence</span></span>
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2950
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<pre style="margin: 0;"> <span id="LC2950" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// conditions, it's probably pointless to continue with single-precision</span></span>
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<pre style="margin: 0;"> <span id="LC2951" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// arithmetic. (possible todo: use a fully-double-precision routine to</span></span>
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<pre style="margin: 0;"> <span id="LC2952" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// finish the job when that happens.)</span></span>
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<pre style="margin: 0;">-<span id="LC2945" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_iter_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">19</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_iter_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">24</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2954" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">gconv</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;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0001</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">xconv</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;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0001</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2956" 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="n" style="color: #333;">lconv</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0001</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">@@ -3049,7 +3057,12 @@ BoolErr FirthRegression(const float* yy, const float* xx, uint32_t sample_ct, ui</td>
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3049
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3057
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<pre style="margin: 0;"> <span id="LC3057" class="line" lang="cpp"> <span class="p">}</span></span>
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3050
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3058
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<pre style="margin: 0;"> <span id="LC3058" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// printf("%.9g %.9g %g %g\n", loglik, loglik_old, dcoef_max, grad_max);</span></span>
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3051
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3059
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<pre style="margin: 0;"> <span id="LC3059" 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="n" style="color: #333;">loglik_change</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loglik</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">loglik_old</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3052
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<td class="diff-line-num new_line old" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3052" class="line" lang="cpp"> <span class="n" style="color: #333;">is_last_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">iter_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_iter_m1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">loglik_change</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lconv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">delta_and_grad_converged</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hs_bail</span><span class="p">));</span></span>
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3060
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">loglik_change</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lconv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">delta_and_grad_converged</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hs_bail</span><span class="p">))</span> <span class="p">{</span></span>
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3061
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<pre style="margin: 0;">+<span id="LC3061" class="line" lang="cpp"> <span class="n" style="color: #333;">is_last_iter</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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3062
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<pre style="margin: 0;">+<span id="LC3062" 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;">iter_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_iter_m1</span><span class="p">)</span> <span class="p">{</span></span>
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3063
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<pre style="margin: 0;">+<span id="LC3063" class="line" lang="cpp"> <span class="n" style="color: #333;">is_last_iter</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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3064
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<pre style="margin: 0;">+<span id="LC3064" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">is_unfinished_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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3065
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<pre style="margin: 0;">+<span id="LC3065" class="line" lang="cpp"> <span class="p">}</span></span>
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3053
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3066
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<pre style="margin: 0;"> <span id="LC3066" class="line" lang="cpp"> <span class="p">}</span></span>
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3054
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3067
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<pre style="margin: 0;"> <span id="LC3067" class="line" lang="cpp"><span class="p">}</span></span>
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3055
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3068
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<pre style="margin: 0;"> <span id="LC3068" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3159,7 +3172,8 @@ typedef struct {</td>
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3159
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3172
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<pre style="margin: 0;"> <span id="LC3172" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allele_obs_ct</span><span class="p">;</span></span>
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3160
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3173
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<pre style="margin: 0;"> <span id="LC3173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a1_dosage</span><span class="p">;</span></span>
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3161
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3174
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<pre style="margin: 0;"> <span id="LC3174" class="line" lang="cpp"></span>
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3162
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<pre style="margin: 0;">-<span id="LC3162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">firth_fallback</span><span class="p">;</span></span>
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3175
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<pre style="margin: 0;">+<span id="LC3175" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">firth_fallback</span><span class="p">;</span></span>
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3176
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<pre style="margin: 0;">+<span id="LC3176" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">is_unfinished</span><span class="p">;</span></span>
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3163
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3177
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<pre style="margin: 0;"> <span id="LC3177" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">case_allele_obs_ct</span><span class="p">;</span></span>
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3178
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<pre style="margin: 0;"> <span id="LC3178" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a1_case_dosage</span><span class="p">;</span></span>
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3179
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<pre style="margin: 0;"> <span id="LC3179" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3671,12 +3685,13 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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3671
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3685
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<pre style="margin: 0;"> <span id="LC3685" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --xchr-model 1 corner case.)</span></span>
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3672
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3686
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<pre style="margin: 0;"> <span id="LC3686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pgv</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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3673
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3687
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<pre style="margin: 0;"> <span id="LC3687" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span 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="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3674
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<pre style="margin: 0;">-<span id="LC3674" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// equivalent to SetBit(1 - omitted_allele_idx, const_alleles);</span></span>
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3675
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<pre style="margin: 0;">-<span id="LC3675" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">omitted_allele_idx</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3688" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (28 Mar 2020): didn't set the bit that actually</span></span>
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3689
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<pre style="margin: 0;">+<span id="LC3689" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// mattered last week...</span></span>
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<pre style="margin: 0;">+<span id="LC3690" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;">3</span><span class="p">;</span></span>
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3676
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3691
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<pre style="margin: 0;"> <span id="LC3691" class="line" lang="cpp"> <span class="p">}</span></span>
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3677
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3692
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<pre style="margin: 0;"> <span id="LC3692" 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;">pgv</span><span class="p">.</span><span class="n" style="color: #333;">dosage_ct</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="p">{</span></span>
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3678
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3693
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<pre style="margin: 0;"> <span id="LC3693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">DosageIsConstant</span><span class="p">(</span><span class="n" style="color: #333;">dosage_sum</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_ssq</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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3679
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<pre style="margin: 0;">-<span id="LC3679" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left">2</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">omitted_allele_idx</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3694" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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3695
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<pre style="margin: 0;"> <span id="LC3695" class="line" lang="cpp"> <span class="p">}</span></span>
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3696
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<pre style="margin: 0;"> <span id="LC3696" class="line" lang="cpp"> <span class="p">}</span></span>
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3697
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<pre style="margin: 0;"> <span id="LC3697" class="line" lang="cpp"> <span class="n" style="color: #333;">machr2_dosage_sums</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">omitted_allele_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dosage_sum</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">@@ -4045,6 +4060,7 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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4045
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<pre style="margin: 0;"> <span id="LC4060" class="line" lang="cpp"></span>
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4046
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<td class="diff-line-num new_line" data-linenumber="4061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4061
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<pre style="margin: 0;"> <span id="LC4061" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">nonomitted_allele_idx</span><span class="p">].</span><span class="n" style="color: #333;">a1_case_dosage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a1_case_dosage</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4047
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<td class="diff-line-num new_line" data-linenumber="4062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4062
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<pre style="margin: 0;"> <span id="LC4062" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">nonomitted_allele_idx</span><span class="p">].</span><span class="n" style="color: #333;">firth_fallback</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4048" style="width: 35px; color: rgba(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="4063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4063
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<pre style="margin: 0;">+<span id="LC4063" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">nonomitted_allele_idx</span><span class="p">].</span><span class="n" style="color: #333;">is_unfinished</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="4048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4048
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<td class="diff-line-num new_line" data-linenumber="4064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4064
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<pre style="margin: 0;"> <span id="LC4064" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">nonomitted_allele_idx</span><span class="p">].</span><span class="n" style="color: #333;">mach_r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mach_r2</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4049
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<td class="diff-line-num new_line" data-linenumber="4065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4065
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<pre style="margin: 0;"> <span id="LC4065" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nonomitted_allele_idx</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4050
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<td class="diff-line-num new_line" data-linenumber="4066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4066
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<pre style="margin: 0;"> <span id="LC4066" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4172" style="width: 35px; color: rgba(0,0,0,0.3); 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="4188" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4172,6 +4188,7 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="4172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4172
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<td class="diff-line-num new_line" data-linenumber="4188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4188
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<pre style="margin: 0;"> <span id="LC4188" 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;">extra_regression_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;">extra_regression_idx</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">extra_regression_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">extra_regression_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4173
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<td class="diff-line-num new_line" data-linenumber="4189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4189
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<pre style="margin: 0;"> <span id="LC4189" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">main_vals</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;">nm_predictors_pmaj_buf</span><span class="p">[</span><span class="n" style="color: #333;">nm_sample_ctav</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4174
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<td class="diff-line-num new_line" data-linenumber="4190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4190
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<pre style="margin: 0;"> <span id="LC4190" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">domdev_vals</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 old_line" data-linenumber="4175" style="width: 35px; color: rgba(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="4191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4191
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<pre style="margin: 0;">+<span id="LC4191" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">is_unfinished</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="4175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4175
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<td class="diff-line-num new_line" data-linenumber="4192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4192
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<pre style="margin: 0;"> <span id="LC4192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extra_regression_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4176
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<td class="diff-line-num new_line" data-linenumber="4193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4193
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<pre style="margin: 0;"> <span id="LC4193" 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;">const_alleles</span><span class="p">,</span> <span class="n" style="color: #333;">extra_regression_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">extra_regression_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">omitted_allele_idx</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4177
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<td class="diff-line-num new_line" data-linenumber="4194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4194
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<pre style="margin: 0;"> <span id="LC4194" class="line" lang="cpp"> <span class="n" style="color: #333;">glm_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SetGlmErr0</span><span class="p">(</span><span class="n" style="color: #333;">kGlmErrcodeConstAllele</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); 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="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4308,7 +4325,7 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4308
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<td class="diff-line-num new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4325
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<pre style="margin: 0;"> <span id="LC4325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">GlmLogisticThread_skip_regression</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4309
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<td class="diff-line-num new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4326
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<pre style="margin: 0;"> <span id="LC4326" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4310
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<td class="diff-line-num new_line" data-linenumber="4327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4327
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<pre style="margin: 0;"> <span id="LC4327" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4311
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<td class="diff-line-num new_line old" data-linenumber="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LogisticRegression</span><span class="p">(</span><span class="n" style="color: #333;">nm_pheno_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_predictors_pmaj_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">cur_predictor_ct</span><span class="p">,</span> <span class="n" style="color: #333;">coef_return</span><span class="p">,</span> <span class="n" style="color: #333;">cholesky_decomp_return</span><span class="p">,</span> <span class="n" style="color: #333;">pp_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_variance_buf</span><span class="p">,</span> <span class="n" style="color: #333;">hh_return</span><span class="p">,</span> <span class="n" style="color: #333;">gradient_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dcoef_buf</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4312" style="width: 35px; color: rgba(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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4328
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<pre style="margin: 0;">+<span id="LC4328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">LogisticRegression</span><span class="p">(</span><span class="n" style="color: #333;">nm_pheno_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_predictors_pmaj_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">cur_predictor_ct</span><span class="p">,</span> <span class="n" style="color: #333;">coef_return</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">is_unfinished</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">cholesky_decomp_return</span><span class="p">,</span> <span class="n" style="color: #333;">pp_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_variance_buf</span><span class="p">,</span> <span class="n" style="color: #333;">hh_return</span><span class="p">,</span> <span class="n" style="color: #333;">gradient_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dcoef_buf</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4312
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<td class="diff-line-num new_line" data-linenumber="4329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4329
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<pre style="margin: 0;"> <span id="LC4329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_sometimes_firth</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4313
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<td class="diff-line-num new_line" data-linenumber="4330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4330
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<pre style="margin: 0;"> <span id="LC4330" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroFArr</span><span class="p">(</span><span class="n" style="color: #333;">cur_predictor_ctav</span><span class="p">,</span> <span class="n" style="color: #333;">coef_return</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4314
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<td class="diff-line-num new_line" data-linenumber="4331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4331
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<pre style="margin: 0;"> <span id="LC4331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">GlmLogisticThread_firth_fallback</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4357" style="width: 35px; color: rgba(0,0,0,0.3); 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="4374" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4357,7 +4374,7 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="4357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4357
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<td class="diff-line-num new_line" data-linenumber="4374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4374
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<pre style="margin: 0;"> <span id="LC4374" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4358
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<td class="diff-line-num new_line" data-linenumber="4375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4375
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<pre style="margin: 0;"> <span id="LC4375" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4359
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<td class="diff-line-num new_line" data-linenumber="4376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4376
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<pre style="margin: 0;"> <span id="LC4376" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4360
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<td class="diff-line-num new_line old" data-linenumber="4377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FirthRegression</span><span class="p">(</span><span class="n" style="color: #333;">nm_pheno_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_predictors_pmaj_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">cur_predictor_ct</span><span class="p">,</span> <span class="n" style="color: #333;">coef_return</span><span class="p">,</span> <span class="n" style="color: #333;">hh_return</span><span class="p">,</span> <span class="n" style="color: #333;">inverse_corr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">inv_1d_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dbl_2d_buf</span><span class="p">,</span> <span class="n" style="color: #333;">pp_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_variance_buf</span><span class="p">,</span> <span class="n" style="color: #333;">gradient_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dcoef_buf</span><span class="p">,</span> <span class="n" style="color: #333;">score_buf</span><span class="p">,</span> <span class="n" style="color: #333;">tmpnxk_buf</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4361" style="width: 35px; color: rgba(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="4377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4377
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<pre style="margin: 0;">+<span id="LC4377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FirthRegression</span><span class="p">(</span><span class="n" style="color: #333;">nm_pheno_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_predictors_pmaj_buf</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">cur_predictor_ct</span><span class="p">,</span> <span class="n" style="color: #333;">coef_return</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">is_unfinished</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">hh_return</span><span class="p">,</span> <span class="n" style="color: #333;">inverse_corr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">inv_1d_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dbl_2d_buf</span><span class="p">,</span> <span class="n" style="color: #333;">pp_buf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_variance_buf</span><span class="p">,</span> <span class="n" style="color: #333;">gradient_buf</span><span class="p">,</span> <span class="n" style="color: #333;">dcoef_buf</span><span class="p">,</span> <span class="n" style="color: #333;">score_buf</span><span class="p">,</span> <span class="n" style="color: #333;">tmpnxk_buf</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4361
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<td class="diff-line-num new_line" data-linenumber="4378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4378
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<pre style="margin: 0;"> <span id="LC4378" class="line" lang="cpp"> <span class="n" style="color: #333;">glm_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SetGlmErr0</span><span class="p">(</span><span class="n" style="color: #333;">kGlmErrcodeFirthConvergeFail</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4362
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<td class="diff-line-num new_line" data-linenumber="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4379
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<pre style="margin: 0;"> <span id="LC4379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">GlmLogisticThread_skip_regression</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4363
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<td class="diff-line-num new_line" data-linenumber="4380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4380
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<pre style="margin: 0;"> <span id="LC4380" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4384" style="width: 35px; color: rgba(0,0,0,0.3); 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="4401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4384,6 +4401,14 @@ THREAD_FUNC_DECL GlmLogisticThread(void* raw_arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="4384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4384
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<td class="diff-line-num new_line" data-linenumber="4401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4401
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<pre style="margin: 0;"> <span id="LC4401" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4385
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<td class="diff-line-num new_line" data-linenumber="4402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4402
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<pre style="margin: 0;"> <span id="LC4402" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4386
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<td class="diff-line-num new_line" data-linenumber="4403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4403
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<pre style="margin: 0;"> <span id="LC4403" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4387" style="width: 35px; color: rgba(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="4404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4404
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<pre style="margin: 0;">+<span id="LC4404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_unfinished</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4387" style="width: 35px; color: rgba(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="4405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4405
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<pre style="margin: 0;">+<span id="LC4405" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">extra_regression_idx</span><span class="p">].</span><span class="n" style="color: #333;">is_unfinished</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4387" style="width: 35px; color: rgba(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="4406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4406
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<pre style="margin: 0;">+<span id="LC4406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele_ct_m2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">beta_se_multiallelic_fused</span><span class="p">)</span> <span class="p">{</span></span>
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4407
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<pre style="margin: 0;">+<span id="LC4407" 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;">1</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;">allele_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uii</span><span class="p">)</span> <span class="p">{</span></span>
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4408
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<pre style="margin: 0;">+<span id="LC4408" class="line" lang="cpp"> <span class="n" style="color: #333;">block_aux_iter</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">].</span><span class="n" style="color: #333;">is_unfinished</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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4409
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<pre style="margin: 0;">+<span id="LC4409" class="line" lang="cpp"> <span class="p">}</span></span>
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4410
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<pre style="margin: 0;">+<span id="LC4410" class="line" lang="cpp"> <span class="p">}</span></span>
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4411
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<pre style="margin: 0;">+<span id="LC4411" class="line" lang="cpp"> <span class="p">}</span></span>
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4387
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4412
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<pre style="margin: 0;"> <span id="LC4412" class="line" lang="cpp"> <span class="p">{</span></span>
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4388
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4413
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<pre style="margin: 0;"> <span id="LC4413" class="line" lang="cpp"> <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;">beta_se_iter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beta_se_iter</span><span class="p">;</span></span>
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4389
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<td class="diff-line-num new_line" data-linenumber="4414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4414
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<pre style="margin: 0;"> <span id="LC4414" 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;">pred_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reported_pred_uidx_start</span><span class="p">;</span> <span class="n" style="color: #333;">pred_uidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">reported_pred_uidx_biallelic_end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pred_uidx</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="6183" style="width: 35px; color: rgba(0,0,0,0.3); 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="6208" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6183,7 +6208,11 @@ PglErr GlmLogistic(const char* cur_pheno_name, const char* const* test_names, co</td>
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6183
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6208
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<pre style="margin: 0;"> <span id="LC6208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">err_col</span><span class="p">)</span> <span class="p">{</span></span>
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6184
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6209
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<pre style="margin: 0;"> <span id="LC6209" 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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6185
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6210
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<pre style="margin: 0;"> <span id="LC6210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">test_is_valid</span><span class="p">)</span> <span class="p">{</span></span>
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6186
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<pre style="margin: 0;">-<span id="LC6186" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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6211
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<pre style="margin: 0;">+<span id="LC6211" 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;">auxp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_unfinished</span><span class="p">)</span> <span class="p">{</span></span>
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6212
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<pre style="margin: 0;">+<span id="LC6212" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cswritep</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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6213
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<pre style="margin: 0;">+<span id="LC6213" 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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6214
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<pre style="margin: 0;">+<span id="LC6214" class="line" lang="cpp"> <span class="n" style="color: #333;">cswritep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">cswritep</span><span class="p">,</span> <span class="s" style="color: #d14;">"UNFINISHED"</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="p">}</span></span>
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6187
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6216
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<pre style="margin: 0;"> <span id="LC6216" 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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6188
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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;">uint64_t</span> <span class="n" style="color: #333;">glm_errcode</span><span class="p">;</span></span>
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6189
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<td class="diff-line-num new_line" data-linenumber="6218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6218
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<pre style="margin: 0;"> <span id="LC6218" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">glm_errcode</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">beta_se_iter</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;">test_idx</span><span class="p">]),</span> <span class="mi" style="color: #099;">8</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">@@ -6786,11 +6815,11 @@ THREAD_FUNC_DECL GlmLinearThread(void* raw_arg) {</td>
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6786
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6815
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<pre style="margin: 0;"> <span id="LC6815" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --xchr-model 1 corner case.)</span></span>
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6787
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6816
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<pre style="margin: 0;"> <span id="LC6816" 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;">pgv</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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6788
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6817
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<pre style="margin: 0;"> <span id="LC6817" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span 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="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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6789
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<pre style="margin: 0;">-<span id="LC6789" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left">2</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">omitted_allele_idx</span></span><span class="p">;</span></span>
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6818
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<pre style="margin: 0;">+<span id="LC6818" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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6790
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6819
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<pre style="margin: 0;"> <span id="LC6819" class="line" lang="cpp"> <span class="p">}</span></span>
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6791
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6820
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<pre style="margin: 0;"> <span id="LC6820" 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;">pgv</span><span class="p">.</span><span class="n" style="color: #333;">dosage_ct</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="p">{</span></span>
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6792
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6821
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<pre style="margin: 0;"> <span id="LC6821" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">DosageIsConstant</span><span class="p">(</span><span class="n" style="color: #333;">dosage_sum</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_ssq</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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6793
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<pre style="margin: 0;">-<span id="LC6793" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left">2</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">omitted_allele_idx</span></span><span class="p">;</span></span>
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6822
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<pre style="margin: 0;">+<span id="LC6822" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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6794
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6823
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<pre style="margin: 0;"> <span id="LC6823" class="line" lang="cpp"> <span class="p">}</span></span>
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6795
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6824
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<pre style="margin: 0;"> <span id="LC6824" class="line" lang="cpp"> <span class="p">}</span></span>
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6796
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6825
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<pre style="margin: 0;"> <span id="LC6825" class="line" lang="cpp"> <span class="n" style="color: #333;">machr2_dosage_sums</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">omitted_allele_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dosage_sum</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8849" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -8849,11 +8878,11 @@ THREAD_FUNC_DECL GlmLinearSubbatchThread(void* raw_arg) {</td>
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8849
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8878
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<pre style="margin: 0;"> <span id="LC8878" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// --xchr-model 1 corner case.)</span></span>
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8850
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8879
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<pre style="margin: 0;"> <span id="LC8879" 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;">pgv</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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8851
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8880
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<pre style="margin: 0;"> <span id="LC8880" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span 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="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">genocounts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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8852
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<pre style="margin: 0;">-<span id="LC8852" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left">2</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">omitted_allele_idx</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC8881" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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8853
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8882
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<pre style="margin: 0;"> <span id="LC8882" class="line" lang="cpp"> <span class="p">}</span></span>
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8854
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8883
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<pre style="margin: 0;"> <span id="LC8883" 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;">pgv</span><span class="p">.</span><span class="n" style="color: #333;">dosage_ct</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="p">{</span></span>
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8855
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8884
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<pre style="margin: 0;"> <span id="LC8884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">DosageIsConstant</span><span class="p">(</span><span class="n" style="color: #333;">dosage_sum</span><span class="p">,</span> <span class="n" style="color: #333;">dosage_ssq</span><span class="p">,</span> <span class="n" style="color: #333;">nm_sample_ct</span><span class="p">))</span> <span class="p">{</span></span>
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8856
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<pre style="margin: 0;">-<span id="LC8856" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left">2</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">omitted_allele_idx</span></span><span class="p">;</span></span>
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8885
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<pre style="margin: 0;">+<span id="LC8885" class="line" lang="cpp"> <span class="n" style="color: #333;">const_alleles</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;"><span class="idiff left right">3</span></span><span class="p">;</span></span>
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8857
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8886
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<pre style="margin: 0;"> <span id="LC8886" class="line" lang="cpp"> <span class="p">}</span></span>
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8858
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8887
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<pre style="margin: 0;"> <span id="LC8887" class="line" lang="cpp"> <span class="p">}</span></span>
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8859
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8888
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<pre style="margin: 0;"> <span id="LC8888" class="line" lang="cpp"> <span class="n" style="color: #333;">machr2_dosage_sums</span><span class="p">[</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">omitted_allele_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dosage_sum</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10645" style="width: 35px; color: rgba(0,0,0,0.3); 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="10674" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10645,6 +10674,7 @@ PglErr GlmMain(const uintptr_t* orig_sample_include, const SampleIdInfo* siip, c</td>
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10645
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10674
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<pre style="margin: 0;"> <span id="LC10674" class="line" lang="cpp"> <span class="p">}</span></span>
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10646
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10675
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<pre style="margin: 0;"> <span id="LC10675" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">orig_variant_ct</span><span class="p">);</span></span>
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10647
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10676
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<pre style="margin: 0;"> <span id="LC10676" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// common linear/logistic initialization</span></span>
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10677
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<pre style="margin: 0;">+<span id="LC10677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GlmFlags</span> <span class="n" style="color: #333;">glm_flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glm_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span><span class="p">;</span></span>
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10648
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10678
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<pre style="margin: 0;"> <span id="LC10678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">early_variant_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_variant_include</span><span class="p">;</span></span>
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10649
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10679
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<pre style="margin: 0;"> <span id="LC10679" 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;">local_sample_uidx_order</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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10650
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10680
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<pre style="margin: 0;"> <span id="LC10680" 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;">local_variant_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10689" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10659,7 +10689,6 @@ PglErr GlmMain(const uintptr_t* orig_sample_include, const SampleIdInfo* siip, c</td>
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10659
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10689
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<pre style="margin: 0;"> <span id="LC10689" class="line" lang="cpp"> <span class="p">}</span></span>
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10660
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10690
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<pre style="margin: 0;"> <span id="LC10690" class="line" lang="cpp"> <span class="p">}</span></span>
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10661
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10691
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<pre style="margin: 0;"> <span id="LC10691" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC10662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GlmFlags</span> <span class="n" style="color: #333;">glm_flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glm_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span><span class="p">;</span></span>
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10663
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10692
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<pre style="margin: 0;"> <span id="LC10692" class="line" lang="cpp"> <span class="n" style="color: #333;">common</span><span class="p">.</span><span class="n" style="color: #333;">glm_flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glm_flags</span><span class="p">;</span></span>
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10693
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<pre style="margin: 0;"> <span id="LC10693" class="line" lang="cpp"> <span class="n" style="color: #333;">common</span><span class="p">.</span><span class="n" style="color: #333;">dosage_presents</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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10694
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<pre style="margin: 0;"> <span id="LC10694" class="line" lang="cpp"> <span class="n" style="color: #333;">common</span><span class="p">.</span><span class="n" style="color: #333;">dosage_mains</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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<a href="https://salsa.debian.org/med-team/plink2/-/commit/394d8a281efdc53907dca6c9cc8dbb8c15317766#2a4cda92f206bc9a46e7c7168314aa0fad145d68"><strong>plink2_glm.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,9 +115,9 @@ void CleanupGlm(GlmInfo* glm_info_ptr);</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// for testing purposes</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// plink2_matrix.h must be included in this file</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BoolErr LogisticRegression(const float* yy, const float* xx, uint32_t sample_ct, uint32_t predictor_ct, float* coef, <span class="idiff left right">float* ll, float* pp, float* vv, float* hh, float* grad, float* dcoef);</span></span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BoolErr LogisticRegression(const float* yy, const float* xx, uint32_t sample_ct, uint32_t predictor_ct, float* coef, <span class="idiff left right">uint32_t* is_unfinished_ptr, float* ll, float* pp, float* vv, float* hh, float* grad, float* dcoef) {</span></span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BoolErr FirthRegression(const float* yy, const float* xx, uint32_t sample_ct, uint32_t predictor_ct, float* coef, <span class="idiff left right">float* hh, matrix_finvert_buf1_t* inv_1d_buf, float* flt_2d_buf, float* pp, float* vv, float* grad, float* dcoef, float* ww, float* tmpnxk_buf);</span></span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// BoolErr FirthRegression(const float* yy, const float* xx, uint32_t sample_ct, uint32_t predictor_ct, float* coef, <span class="idiff left right">uint32_t* is_unfinished_ptr, float* hh, double* half_inverted_buf, MatrixInvertBuf1* inv_1d_buf, double* dbl_2d_buf, float* pp, float* vv, float* grad, float* dcoef, float* ww, float* tmpnxk_buf) {</span></span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">GlmMain</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig_sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covar_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covar_names</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig_variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlleleCode</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">maj_alleles</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GlmInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">glm_info_ptr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AdjustInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">adjust_info_ptr</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">APerm</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aperm_ptr</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;">local_covar_fname</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;">local_pvar_fname</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;">local_psam_fname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">orig_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">orig_covar_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_covar_name_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">orig_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_variant_id_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">xchr_model</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ci_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">vif_thresh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ln_pfilter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">output_min_ln</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">pgr_alloc_cacheline_ct</span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,12 +290,12 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" --make-pgen ['vzs'] ['format='<code>] [{trim-alts | erase-alt2+}]\n"</span></span>
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292
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['erase-phase'] ['erase-dosage'] ['multiallelics='<mode>]\n"</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" [{v<span class="idiff left right">id-split | vid-split-dup | vid-dup | v</span>id-join}]\n"</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" [{v<span class="idiff left right">arid-split | varid-split-dup | varid-dup | var</span>id-join}]\n"</span></span>
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294
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['pvar-cols='<col set descriptor>]\n"</span></span>
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295
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['psam-cols='<col set descriptor>]\n"</span></span>
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296
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" --make-bpgen ['vzs'] ['format='<code>] [{trim-alts | erase-alt2+}]\n"</span></span>
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297
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['erase-phase'] ['erase-dosage'] ['multiallelics='<mode>]\n"</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" [{v<span class="idiff left right">id-split | vid-split-dup | vid-dup | v</span>id-join}]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" [{v<span class="idiff left right">arid-split | varid-split-dup | varid-dup | var</span>id-join}]\n"</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" --make-bed ['vzs'] [{trim-alts | erase-alt2+}]\n"</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ['multiallelics='<split mode>]\n"</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -338,19 +338,21 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" alleles are joined into a single multiallelic variant.\n"</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" Symbolic ALT alleles are joined separately. Additional conditions apply\n"</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" to them, and PLINK 2 usually errors out when they aren't met.\n"</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" When splitting with 'vid-dup', the new variants keep the original variant\n"</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" When splitting with 'varid-dup', the new variants keep the original\n"</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" variant\n"</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" ID. Otherwise, new variant IDs are assigned as follows:\n"</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 1. If --set-all-var-ids was specified, that template is applied.\n"</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 2. Otherwise, if joining, and all source variant IDs are identical and\n"</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" nonmissing, that ID is used.\n"</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 3. Otherwise, if splitting with the 'v<span class="idiff left right">id-split' or 'v</span>id-split-dup'\n"</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 3. Otherwise, if splitting with the 'v<span class="idiff left right">arid-split' or 'var</span>id-split-dup'\n"</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" modifier, the original variant ID is split on the ';' character when\n"</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" the number of ';'s is correct. (When the post-split ID is the missing\n"</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" code, --set-missing-var-ids is applied to it.) Similarly, if joining\n"</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" with the 'vid-join' modifier, the new variant ID is set to the\n"</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" with the 'v<span class="idiff left right">ar</span>id-join' modifier, the new variant ID is set to the\n"</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" original IDs joined with the ';' character when all original IDs are\n"</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" nonmissing and contain exactly one ';' per extra ALT allele.\n"</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 4. Otherwise, if splitting with 'vid-split-dup', the original ID is kept.\n"</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 4. Otherwise, if splitting with 'varid-split-dup', the original ID is\n"</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" kept.\n"</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 5. Otherwise, if --set-missing-var-ids was specified, that template is\n"</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" applied.\n"</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">" 6. Otherwise, the variant ID is set to the missing code.\n"</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">@@ -992,10 +994,10 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"glm</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">linear</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">logistic</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">assoc</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">help_ctrl</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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993
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995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp"><span class="s" style="color: #d14;">" --glm ['zs'] ['omit-ref'] [{sex | no-x-sex}] ['log10'] ['pheno-ids']</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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994
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"><span class="s" style="color: #d14;">" [{genotypic | hethom | dominant | recessive}] ['interaction'] ['skip']</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['hide-covar'] [<span class="idiff left right">'intercept'] [{no-firth | firth-fallback | firth}</span>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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996
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['cols='<col set desc<span class="idiff left right">.</span>>] ['local-covar='<file>] ['local-psam='<file>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['hide-covar'] [<span class="idiff left right">{no-firth | firth-fallback | firth}] ['intercept'</span>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['cols='<col set desc>] ['local-covar='<file>] ['local-psam='<file>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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997
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999
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['local-pos-cols='<key col #s> | 'local-pvar='<file>] ['local-haps']</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="LC998" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['local-omit-last' | 'local-cats[0]='<category ct>]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="cpp"><span class="s" style="color: #d14;">" ['local-omit-last' | 'local-cats[0]='<category ct>]<span class="idiff left right"> ['allow-no-covars']</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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999
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// " ['perm' | 'mperm='<value>] ['perm-count']\n"</span></span>
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1000
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="cpp"><span class="s" style="color: #d14;">" Basic association analysis on quantitative and/or case/control phenotypes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1001
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="cpp"><span class="s" style="color: #d14;">" For each variant, a linear (for quantitative traits) or logistic (for</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1037,6 +1039,10 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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1037
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="cpp"><span class="s" style="color: #d14;">" statistics are reported for all nonconstant predictors; 'hide-covar'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1038
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"><span class="s" style="color: #d14;">" suppresses covariate-only results, while 'intercept' causes intercepts</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1039
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp"><span class="s" style="color: #d14;">" to be reported.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"><span class="s" style="color: #d14;">" Since running --glm without at least e.g. principal component covariates</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"><span class="s" style="color: #d14;">" is usually an analytical mistake, the 'allow-no-covars' modifier is now</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"><span class="s" style="color: #d14;">" required when you're intentionally running --glm without a covariate</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"><span class="s" style="color: #d14;">" file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1040
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp"><span class="s" style="color: #d14;">" * By default, if the current phenotype and covariates are such that every</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1041
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<td class="diff-line-num new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cpp"><span class="s" style="color: #d14;">" regression on a chromosome will fail, PLINK 2 errors out. To just skip</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 old_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1042
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<td class="diff-line-num new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp"><span class="s" style="color: #d14;">" the phenotype or chromosome instead, add the 'skip' modifier.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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