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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d">b3bdaa5c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-17T10:00:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-210116+dfsg</pre>
</li>
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<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
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<li class="file-stats">
<a href="#5c0ac48ba397674ac28142efc3b29b7de442d076">
plink2_cmdline.cc
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<li class="file-stats">
<a href="#353424a9b88ab7aad403c3734bdd60f28af6b661">
plink2_cmdline.h
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<li class="file-stats">
<a href="#8abb94ca0fef8a58740274abf79b38fd70201601">
plink2_common.cc
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<li class="file-stats">
<a href="#576e4fd14d1d66b779bb9f5d05d29f2871392d1a">
plink2_common.h
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<li class="file-stats">
<a href="#49a9b8ad832d31a64af7997ab4dff296fe4603bc">
plink2_data.cc
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<li class="file-stats">
<a href="#a125279a9188813c60a6fe3d56cead0bd36fcc8f">
plink2_data.h
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<li class="file-stats">
<a href="#0bb44e45468b97ef0c21ed5ca6767a690fbf6626">
plink2_export.cc
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<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
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<li class="file-stats">
<a href="#21274e2b169d6e71a254a974b86ae7af8acdf275">
plink2_import.cc
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<li class="file-stats">
<a href="#77152f1b1412f42b6493e48b39abf3be847a626f">
plink2_merge.cc
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<li class="file-stats">
<a href="#59216b3409d1d2c9ff4b9a784709ac15d3a3e12c">
plink2_merge.h
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<li class="file-stats">
<a href="#68ec2c295201ac9d061fcfc37744eba392732614">
plink2_misc.cc
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<li class="file-stats">
<a href="#436d5ebb95c2149ac987678ddff33cffca2ea965">
plink2_psam.cc
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<li class="file-stats">
<a href="#c213d6a8351bbee48c82c7a6399fd1202e28bf94">
plink2_psam.h
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</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6,8 +6,8 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Does not currently support -DCPU_CHECK_...</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">BASEFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-DZSTD_MULTITHREAD</span> <span class="nt" style="color: #000080;">-DSTATIC_ZSTD</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>BASEFLAGS=-g -DZSTD_MULTITHREAD -DSTATIC_ZSTD</span></span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">BASEFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-mavx2</span> <span class="nt" style="color: #000080;">-mbmi</span> <span class="nt" style="color: #000080;">-mbmi2</span> <span class="nt" style="color: #000080;">-mlzcnt</span> <span class="nt" style="color: #000080;">-DZSTD_MULTITHREAD</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> Makefile.src</span></span>
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<li id="e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f"><strong>plink2.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -71,10 +71,10 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="">#ifdef USE_MKL</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang=""> " Intel"</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="">#endif</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang=""> " (<span class="idiff left right">4</span> Jan 2021)";</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang=""> " (<span class="idiff left right">16</span> Jan 2021)";</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="">static const char ver_str2[] =</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang=""> "<span class="idiff left right"> </span>"</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang=""> ""</span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="">#ifndef LAPACK_ILP64</span>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang=""> " "</span>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="">#endif</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -286,8 +286,8 @@ typedef struct Plink2CmdlineStruct {</td>
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286
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang=""></span>
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287
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang=""> Command1Flags command_flags1;</span>
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288
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang=""> PvarPsamFlags pvar_psam_flags;</span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang=""> Sort<span class="idiff left right">Flags sample_sort_flags</span>;</span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang=""> Sort<span class="idiff left right">Flags sort_vars_flags</span>;</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang=""> Sort<span class="idiff left right">Mode sample_sort_mode</span>;</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang=""> Sort<span class="idiff left right">Mode sort_vars_mode</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=""> GrmFlags grm_flags;</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=""> PcaFlags pca_flags;</span>
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293
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang=""> WriteCovarFlags write_covar_flags;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); 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="1363" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1363,6 +1363,8 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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1363
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang=""> if (unlikely(reterr)) {</span>
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1364
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang=""> goto Plink2Core_ret_1;</span>
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1365
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1365
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang=""> }</span>
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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang=""> // bugfix (16 Jan 2021)</span>
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1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang=""> pii.sii.flags |= kfSampleIdParentsPresent;</span>
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1366
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang=""> }</span>
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1367
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1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang=""> }</span>
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1368
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang=""> // --update-parents goes here</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2502" style="width: 35px; color: rgba(0,0,0,0.3); 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="2504" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2502,11 +2504,11 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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2502
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2504
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<pre style="margin: 0;"> <span id="LC2504" class="line" lang=""> BigstackReset(bigstack_mark_allele_ddosages);</span>
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2503
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<td class="diff-line-num new_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2505
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2505" class="line" lang=""></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2504
</td>
<td class="diff-line-num new_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2506
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2506" class="line" lang=""> uint32_t* new_sample_idx_to_old = nullptr;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2505
</td>
<td class="diff-line-num new_line old" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC2505" class="line" lang=""> if (pcp->sample_sort_<span class="idiff left right">flags & (kfSortNatural | kfSortAscii | kfSortFile)</span>) {</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2507
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2507" class="line" lang=""> if (pcp->sample_sort_<span class="idiff left right">mode > kSortNone</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="2506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2506
</td>
<td class="diff-line-num new_line" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2508
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2508" class="line" lang=""> if (sample_ct < 2) {</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="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2507
</td>
<td class="diff-line-num new_line" data-linenumber="2509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2509
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2509" class="line" lang=""> logerrputs("Warning: Skipping --sample-sort since <2 samples are present.\n");</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="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2508
</td>
<td class="diff-line-num new_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2510
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2510" class="line" lang=""> } else {</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="2509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2509
</td>
<td class="diff-line-num new_line old" data-linenumber="2511" style="width: 35px; color: rgba(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="LC2509" class="line" lang=""> if (pcp->sample_sort_<span class="idiff left right">flags & kf</span>SortFile) {</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="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2511
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2511" class="line" lang=""> if (pcp->sample_sort_<span class="idiff left right">mode == k</span>SortFile) {</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2510
</td>
<td class="diff-line-num new_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2512
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2512" class="line" lang=""> reterr = SampleSortFileMap(sample_include, &pii.sii, pcp->sample_sort_fname, raw_sample_ct, sample_ct, &new_sample_idx_to_old);</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2511
</td>
<td class="diff-line-num new_line" data-linenumber="2513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2513
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2513" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2512
</td>
<td class="diff-line-num new_line" data-linenumber="2514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2514
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2514" class="line" lang=""> goto Plink2Core_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); 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="2519" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2517,7 +2519,7 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2517
</td>
<td class="diff-line-num new_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2519" class="line" lang=""> // to spare here, so keep the code simpler for now</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2518
</td>
<td class="diff-line-num new_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2520
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2520" class="line" lang=""> char* sorted_xidbox_tmp;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
</td>
<td class="diff-line-num new_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2521" class="line" lang=""> uintptr_t max_xid_blen;</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="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2520
</td>
<td class="diff-line-num new_line old" data-linenumber="2522" style="width: 35px; color: rgba(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="LC2520" class="line" lang=""> reterr = SortedXidboxInitAlloc(sample_include, &pii.sii, sample_ct, 0, pii.sii.sids? kfXidModeFidIidSid : kfXidModeFidIid, (pcp->sample_sort_<span class="idiff left right">flags == kf</span>SortNatural), &sorted_xidbox_tmp, &new_sample_idx_to_old, &max_xid_blen);</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="2521" style="width: 35px; color: rgba(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="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2522
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2522" class="line" lang=""> reterr = SortedXidboxInitAlloc(sample_include, &pii.sii, sample_ct, 0, pii.sii.sids? kfXidModeFidIidSid : kfXidModeFidIid, (pcp->sample_sort_<span class="idiff left right">mode == k</span>SortNatural), &sorted_xidbox_tmp, &new_sample_idx_to_old, &max_xid_blen);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
</td>
<td class="diff-line-num new_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2523" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2522
</td>
<td class="diff-line-num new_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2524
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2524" class="line" lang=""> goto Plink2Core_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
</td>
<td class="diff-line-num new_line" data-linenumber="2525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2525
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2525" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2544,8 +2546,8 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2544
</td>
<td class="diff-line-num new_line" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2546
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2546" class="line" lang=""></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2545
</td>
<td class="diff-line-num new_line" data-linenumber="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2547
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2547" class="line" lang=""> if (pcp->command_flags1 & kfCommand1MakePlink2) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2546
</td>
<td class="diff-line-num new_line" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2548
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2548" class="line" lang=""> // todo: unsorted case (--update-chr, etc.)</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="2547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2547
</td>
<td class="diff-line-num new_line old" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2547" class="line" lang=""> if (pcp->sort_vars_<span class="idiff left right">flags != kfSort0</span>) {</span>
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<td class="diff-line-num old old_line" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2548
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<td class="diff-line-num new_line old" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2548" class="line" lang=""> reterr = MakePlink2Vsort(sample_include, &pii, sex_nm, sex_male, pheno_cols, pheno_names, new_sample_idx_to_old, variant_include, cip, variant_bps, variant_ids, allele_idx_offsets, allele_storage, allele_presents, refalt1_select, pvar_qual_present, pvar_quals, pvar_filter_present, pvar_filter_npass, pvar_filter_storage, info_reload_slen? pvarname : nullptr, variant_cms, chr_idxs, xheader_blen, info_flags, raw_sample_ct, sample_ct, pheno_ct, max_pheno_name_blen, raw_variant_ct, variant_ct, max_allele_ct, max_allele_slen, max_filter_slen, info_reload_slen, pcp->max_thread_ct, pcp->hard_call_thresh, pcp->dosage_erase_thresh, make_plink2_flags, (pcp->sort_vars_<span class="idiff left right">flags == kf</span>SortNatural), pcp->pvar_psam_flags, xheader, &simple_pgr, outname, outname_end);</span>
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<td class="diff-line-num new new_line" data-linenumber="2549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2549
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<pre style="margin: 0;">+<span id="LC2549" class="line" lang=""> if (pcp->sort_vars_<span class="idiff left right">mode > kSortNone</span>) {</span>
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<td class="diff-line-num new new_line" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2550
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<pre style="margin: 0;">+<span id="LC2550" class="line" lang=""> reterr = MakePlink2Vsort(sample_include, &pii, sex_nm, sex_male, pheno_cols, pheno_names, new_sample_idx_to_old, variant_include, cip, variant_bps, variant_ids, allele_idx_offsets, allele_storage, allele_presents, refalt1_select, pvar_qual_present, pvar_quals, pvar_filter_present, pvar_filter_npass, pvar_filter_storage, info_reload_slen? pvarname : nullptr, variant_cms, chr_idxs, xheader_blen, info_flags, raw_sample_ct, sample_ct, pheno_ct, max_pheno_name_blen, raw_variant_ct, variant_ct, max_allele_ct, max_allele_slen, max_filter_slen, info_reload_slen, pcp->max_thread_ct, pcp->hard_call_thresh, pcp->dosage_erase_thresh, make_plink2_flags, (pcp->sort_vars_<span class="idiff left right">mode == k</span>SortNatural), pcp->pvar_psam_flags, xheader, &simple_pgr, outname, outname_end);</span>
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2549
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2551
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<pre style="margin: 0;"> <span id="LC2551" class="line" lang=""> } else {</span>
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2550
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2552
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<pre style="margin: 0;"> <span id="LC2552" class="line" lang=""> if (vpos_sortstatus & kfUnsortedVarBp) {</span>
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2551
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2553
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<pre style="margin: 0;"> <span id="LC2553" class="line" lang=""> logerrputs("Warning: Variants are not sorted by position. Consider rerunning with the\n--sort-vars flag added to remedy this.\n");</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3530" style="width: 35px; color: rgba(0,0,0,0.3); 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="3532" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3530,8 +3532,8 @@ int main(int argc, char** argv) {</td>
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3530
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3532
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<pre style="margin: 0;"> <span id="LC3532" class="line" lang=""> // uint64_t command_flags2 = 0;</span>
</pre>
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3531
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3533
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<pre style="margin: 0;"> <span id="LC3533" class="line" lang=""> pc.misc_flags = kfMisc0;</span>
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3532
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<td class="diff-line-num new_line" data-linenumber="3534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3534
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<pre style="margin: 0;"> <span id="LC3534" class="line" lang=""> pc.pvar_psam_flags = kfPvarPsam0;</span>
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3533
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<pre style="margin: 0;">-<span id="LC3533" class="line" lang=""> pc.sample_sort_<span class="idiff left right">flags = kf</span>Sort0;</span>
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3534
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<pre style="margin: 0;">-<span id="LC3534" class="line" lang=""> pc.sort_vars_<span class="idiff left right">flags = kf</span>Sort0;</span>
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3535
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<pre style="margin: 0;">+<span id="LC3535" class="line" lang=""> pc.sample_sort_<span class="idiff left right">mode = k</span>Sort0;</span>
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3536
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<pre style="margin: 0;">+<span id="LC3536" class="line" lang=""> pc.sort_vars_<span class="idiff left right">mode = k</span>Sort0;</span>
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3535
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3537
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<pre style="margin: 0;"> <span id="LC3537" class="line" lang=""> pc.grm_flags = kfGrm0;</span>
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3536
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3538
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<pre style="margin: 0;"> <span id="LC3538" class="line" lang=""> pc.pca_flags = kfPca0;</span>
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3537
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3539
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<pre style="margin: 0;"> <span id="LC3539" class="line" lang=""> pc.write_covar_flags = kfWriteCovar0;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5845" style="width: 35px; color: rgba(0,0,0,0.3); 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="5847" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5845,7 +5847,7 @@ int main(int argc, char** argv) {</td>
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5845
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5847
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<pre style="margin: 0;"> <span id="LC5847" class="line" lang=""></span>
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5846
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5848
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<pre style="margin: 0;"> <span id="LC5848" class="line" lang=""> case 'i':</span>
</pre>
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5847
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5849
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<pre style="margin: 0;"> <span id="LC5849" class="line" lang=""> if (strequal_k_unsafe(flagname_p2, "ndiv-sort")) {</span>
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5848
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<pre style="margin: 0;">-<span id="LC5848" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, <span class="idiff left right">3</span>))) {</span>
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5850
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<pre style="margin: 0;">+<span id="LC5850" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, <span class="idiff left right">2</span>))) {</span>
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5849
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<td class="diff-line-num new_line" data-linenumber="5851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5851
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<pre style="margin: 0;"> <span id="LC5851" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
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5850
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<td class="diff-line-num new_line" data-linenumber="5852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5852
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<pre style="margin: 0;"> <span id="LC5852" class="line" lang=""> }</span>
</pre>
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5851
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<td class="diff-line-num new_line" data-linenumber="5853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5853
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<pre style="margin: 0;"> <span id="LC5853" class="line" lang=""> const char* mode_str = argvk[arg_idx + 1];</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5853,28 +5855,21 @@ int main(int argc, char** argv) {</td>
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5853
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<td class="diff-line-num new_line" data-linenumber="5855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5855
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<pre style="margin: 0;"> <span id="LC5855" class="line" lang=""> const uint32_t mode_slen = strlen(mode_str);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5854
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<td class="diff-line-num new_line" data-linenumber="5856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5856
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<pre style="margin: 0;"> <span id="LC5856" class="line" lang=""> if (strequal_k(mode_str, "0", mode_slen) ||</span>
</pre>
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5855
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<td class="diff-line-num new_line" data-linenumber="5857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5857
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5857" class="line" lang=""> strequal_k(mode_str, "none", mode_slen)) {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5856
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<td class="diff-line-num new_line old" data-linenumber="5858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5856" class="line" lang=""> pc.sample_sort_<span class="idiff left right">flags = kf</span>SortNone;</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="5858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5858
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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="LC5858" class="line" lang=""> pc.sample_sort_<span class="idiff left right">mode = k</span>SortNone;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5857
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<td class="diff-line-num new_line" data-linenumber="5859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5859
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5859" class="line" lang=""> } else if (((mode_slen == 1) && (first_char_upcase_match == 'N')) ||</span>
</pre>
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5858
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<td class="diff-line-num new_line" data-linenumber="5860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5860
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<pre style="margin: 0;"> <span id="LC5860" class="line" lang=""> strequal_k(mode_str, "natural", mode_slen)) {</span>
</pre>
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5859
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<td class="diff-line-num new_line old" data-linenumber="5861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5859" class="line" lang=""> pc.sample_sort_<span class="idiff left right">flags = kf</span>SortNatural;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5860" style="width: 35px; color: rgba(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="5861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5861
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<pre style="margin: 0;">+<span id="LC5861" class="line" lang=""> pc.sample_sort_<span class="idiff left right">mode = k</span>SortNatural;</span>
</pre>
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5860
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<td class="diff-line-num new_line" data-linenumber="5862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5862
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<pre style="margin: 0;"> <span id="LC5862" class="line" lang=""> } else if (((mode_slen == 1) && (first_char_upcase_match == 'A')) ||</span>
</pre>
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5861
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<td class="diff-line-num new_line" data-linenumber="5863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5863
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5863" class="line" lang=""> strequal_k(mode_str, "ascii", mode_slen)) {</span>
</pre>
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5862
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<td class="diff-line-num new_line old" data-linenumber="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5862" class="line" lang=""> pc.sample_sort_<span class="idiff left right">flags = kf</span>SortAscii;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5863" style="width: 35px; color: rgba(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="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5864
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<pre style="margin: 0;">+<span id="LC5864" class="line" lang=""> pc.sample_sort_<span class="idiff left right">mode = k</span>SortAscii;</span>
</pre>
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5863
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<td class="diff-line-num new_line" data-linenumber="5865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5865
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<pre style="margin: 0;"> <span id="LC5865" class="line" lang=""> } else if (likely(((mode_slen == 1) && (first_char_upcase_match == 'F')) ||</span>
</pre>
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5864
</td>
<td class="diff-line-num new_line" data-linenumber="5866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5866
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5866" class="line" lang=""> strequal_k(mode_str, "file", mode_slen))) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5865
</td>
<td class="diff-line-num new_line" data-linenumber="5867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5867
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5867" class="line" lang=""> if (unlikely(param_ct == 1)) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5866
</td>
<td class="diff-line-num new_line" data-linenumber="5868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5868
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5868" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Missing '--indiv-sort %s' filename.\n", mode_str);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5867
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<td class="diff-line-num new_line" data-linenumber="5869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5869
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5869" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="5868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5868
</td>
<td class="diff-line-num new_line" data-linenumber="5870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5870
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5870" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5869
</td>
<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC5869" class="line" lang=""> pc.sample_sort_flags = kfSortFile;</span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="5870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5870
</td>
<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(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="LC5870" class="line" lang=""> uint32_t fname_modif_idx = 2;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5871
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5871" class="line" lang=""> if (param_ct == 3) {</span>
</pre>
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5872
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5872" class="line" lang=""> if (unlikely(CheckExtraParam(&(argvk[arg_idx]), "sid", &fname_modif_idx))) {</span>
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5873
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5873" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
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5874
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5874" class="line" lang=""> }</span>
</pre>
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5875
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5875" class="line" lang=""> pc.sample_sort_flags |= kfSortFileSid;</span>
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5876
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5876" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5877
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<td class="diff-line-num new_line old" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5877" class="line" lang=""> reterr = AllocFname(argvk[arg_idx + fname_modif_idx], flagname_p, 0, &pc.sample_sort_fname);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5871
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<pre style="margin: 0;">+<span id="LC5871" class="line" lang=""> pc.sample_sort_mode = kSortFile;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5878" style="width: 35px; color: rgba(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="5872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5872
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<pre style="margin: 0;">+<span id="LC5872" class="line" lang=""> reterr = AllocFname(argvk[arg_idx + 2], flagname_p, 0, &pc.sample_sort_fname);</span>
</pre>
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5878
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<td class="diff-line-num new_line" data-linenumber="5873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5873
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<pre style="margin: 0;"> <span id="LC5873" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
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5879
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<td class="diff-line-num new_line" data-linenumber="5874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5874
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5874" class="line" lang=""> goto main_ret_1;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5880
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<td class="diff-line-num new_line" data-linenumber="5875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5875
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5875" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5882" style="width: 35px; color: rgba(0,0,0,0.3); 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="5877" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5882,7 +5877,7 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="5882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5882
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<td class="diff-line-num new_line" data-linenumber="5877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5877
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5877" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: '%s' is not a valid mode for --indiv-sort.\n", mode_str);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5883
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<td class="diff-line-num new_line" data-linenumber="5878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5878
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5878" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5884
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<td class="diff-line-num new_line" data-linenumber="5879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5879
</td>
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<pre style="margin: 0;"> <span id="LC5879" class="line" lang=""> }</span>
</pre>
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5885
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<td class="diff-line-num new_line old" data-linenumber="5880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5885" class="line" lang=""> if (unlikely((param_ct > 1) && (<span class="idiff left right">!(pc.sample_sort_flags & kfSortFile)</span>))) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5886" style="width: 35px; color: rgba(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="5880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5880
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<pre style="margin: 0;">+<span id="LC5880" class="line" lang=""> if (unlikely((param_ct > 1) && (<span class="idiff left right">pc.sample_sort_mode != kSortFile</span>))) {</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="5886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5886
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<td class="diff-line-num new_line" data-linenumber="5881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5881
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5881" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: '--indiv-sort %s' does not accept additional arguments.\n", mode_str);</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5887
</td>
<td class="diff-line-num new_line" data-linenumber="5882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5882
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5882" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="5888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5888
</td>
<td class="diff-line-num new_line" data-linenumber="5883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5883
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5883" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7844" style="width: 35px; color: rgba(0,0,0,0.3); 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="7839" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -7844,24 +7839,31 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="7844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7844
</td>
<td class="diff-line-num new_line" data-linenumber="7839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7839
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7839" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --merge-filter-mode argument '%s'.\n", cur_modif);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7845
</td>
<td class="diff-line-num new_line" data-linenumber="7840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7840
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7840" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7846
</td>
<td class="diff-line-num new_line" data-linenumber="7841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7841
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7841" class="line" lang=""> }</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="7847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7847
</td>
<td class="diff-line-num new_line old" data-linenumber="7842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC7847" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-info-sort")) {</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="7848" style="width: 35px; color: rgba(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="7842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7842
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7842" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-info-sort") ||</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="7848" style="width: 35px; color: rgba(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="7843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7843
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7843" class="line" lang=""> strequal_k_unsafe(flagname_p2, "erge-pheno-sort")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7848
</td>
<td class="diff-line-num new_line" data-linenumber="7844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7844
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7844" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</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="7849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7849
</td>
<td class="diff-line-num new_line" data-linenumber="7845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7845
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7845" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</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="7850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7850
</td>
<td class="diff-line-num new_line" data-linenumber="7846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7846
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7846" class="line" lang=""> }</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="7851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7851
</td>
<td class="diff-line-num new_line" data-linenumber="7847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7847
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7847" class="line" lang=""> const char* mode_str = argvk[arg_idx + 1];</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="7852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7852
</td>
<td class="diff-line-num new_line" data-linenumber="7848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7848
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7848" class="line" lang=""> const char first_char_upcase_match = mode_str[0] & 0xdf;</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="7853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7853
</td>
<td class="diff-line-num new_line" data-linenumber="7849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7849
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7849" class="line" lang=""> const uint32_t mode_slen = strlen(mode_str);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7854
</td>
<td class="diff-line-num new_line old" data-linenumber="7850" style="width: 35px; color: rgba(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="LC7854" class="line" lang=""> if (strequal_k(mode_str, "0", mode_slen) ||</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="7855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7855
</td>
<td class="diff-line-num new_line old" data-linenumber="7850" style="width: 35px; color: rgba(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="LC7855" class="line" lang=""> strequal_k(mode_str, "none", mode_slen)) {</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="7856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7856
</td>
<td class="diff-line-num new_line old" data-linenumber="7850" style="width: 35px; color: rgba(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="LC7856" class="line" lang=""> pmerge_info.merge_info_sort = kfSortNone;</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7850
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7850" class="line" lang=""> SortMode sort_mode = kSortNone;</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="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7851
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7851" class="line" lang=""> if (((mode_slen == 1) && (first_char_upcase_match == 'N')) ||</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="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7852
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7852" class="line" lang=""> strequal_k(mode_str, "natural", mode_slen)) {</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="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7853
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7853" class="line" lang=""> sort_mode = kSortNatural;</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7857
</td>
<td class="diff-line-num new_line" data-linenumber="7854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7854
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7854" class="line" lang=""> } else if (((mode_slen == 1) && (first_char_upcase_match == 'A')) ||</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7858
</td>
<td class="diff-line-num new_line" data-linenumber="7855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7855
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7855" class="line" lang=""> strequal_k(mode_str, "ascii", mode_slen)) {</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="7859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7859
</td>
<td class="diff-line-num new_line old" data-linenumber="7856" style="width: 35px; color: rgba(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="LC7859" class="line" lang=""> <span class="idiff left right">pmerge_info.merge_info_sort = kf</span>SortAscii;</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="7860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7860
</td>
<td class="diff-line-num new_line old" data-linenumber="7856" style="width: 35px; color: rgba(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="LC7860" class="line" lang=""> } else if (unlikely(!(<span class="idiff left right">((mode_slen == 1) && (first_char_upcase_match == 'N')</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="7861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7861
</td>
<td class="diff-line-num new_line old" data-linenumber="7856" style="width: 35px; color: rgba(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="LC7861" class="line" lang=""> strequal_k(mode_str, "n<span class="idiff left right">atural</span>", mode_slen)))) {</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="7862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7862
</td>
<td class="diff-line-num new_line old" data-linenumber="7856" style="width: 35px; color: rgba(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="LC7862" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --<span class="idiff left right">merge-info-sort argument '%s'.\n"</span>, mode_str);</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="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7856
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7856" class="line" lang=""> <span class="idiff left right">sort_mode = k</span>SortAscii;</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="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7857
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7857" class="line" lang=""> } else if (unlikely(!(<span class="idiff left right">strequal_k(mode_str, "0", mode_slen</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="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7858
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7858" class="line" lang=""> strequal_k(mode_str, "n<span class="idiff left right">one</span>", mode_slen)))) {</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="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7859
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7859" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: Invalid --<span class="idiff left right">%s argument '%s'.\n", flagname_p</span>, mode_str);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7863
</td>
<td class="diff-line-num new_line" data-linenumber="7860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7860
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7860" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7864
</td>
<td class="diff-line-num new_line" data-linenumber="7861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7861
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7861" class="line" lang=""> }</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="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7862
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7862" class="line" lang=""> if (flagname_p2[5] == 'i') {</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="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7863
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7863" class="line" lang=""> pmerge_info.merge_info_sort = sort_mode;</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="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7864
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7864" class="line" lang=""> } else {</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="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7865
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7865" class="line" lang=""> pmerge_info.merge_pheno_sort = sort_mode;</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="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="7866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7866
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7866" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7865
</td>
<td class="diff-line-num new_line" data-linenumber="7867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7867
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7867" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "erge-max-allele-ct")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7866
</td>
<td class="diff-line-num new_line" data-linenumber="7868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7868
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7868" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 1))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7867
</td>
<td class="diff-line-num new_line" data-linenumber="7869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7869
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7869" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8467" style="width: 35px; color: rgba(0,0,0,0.3); 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="8469" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -8467,7 +8469,6 @@ int main(int argc, char** argv) {</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8467
</td>
<td class="diff-line-num new_line" data-linenumber="8469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8469
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8469" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8468
</td>
<td class="diff-line-num new_line" data-linenumber="8470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8470
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8470" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8469
</td>
<td class="diff-line-num new_line" data-linenumber="8471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8471
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8471" class="line" lang=""> pc.command_flags1 |= kfCommand1Pmerge;</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="8470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8470
</td>
<td class="diff-line-num new_line old" data-linenumber="8472" style="width: 35px; color: rgba(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="LC8470" class="line" lang=""> pc.dependency_flags |= kfFilterAllReq;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8471
</td>
<td class="diff-line-num new_line" data-linenumber="8472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8472
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8472" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "merge-list")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8472
</td>
<td class="diff-line-num new_line" data-linenumber="8473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8473
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8473" class="line" lang=""> if (pc.command_flags1 & kfCommand1Pmerge) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8473
</td>
<td class="diff-line-num new_line" data-linenumber="8474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8474
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8474" class="line" lang=""> logerrputs("Error: --pmerge-list cannot be used with --pmerge.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8518" style="width: 35px; color: rgba(0,0,0,0.3); 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="8519" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -8518,7 +8519,6 @@ int main(int argc, char** argv) {</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8518
</td>
<td class="diff-line-num new_line" data-linenumber="8519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8519
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8519" class="line" lang=""> goto main_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8519
</td>
<td class="diff-line-num new_line" data-linenumber="8520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8520
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8520" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8520
</td>
<td class="diff-line-num new_line" data-linenumber="8521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8521
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8521" class="line" lang=""> pc.command_flags1 |= kfCommand1Pmerge;</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="8521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8521
</td>
<td class="diff-line-num new_line old" data-linenumber="8522" style="width: 35px; color: rgba(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="LC8521" class="line" lang=""> pc.dependency_flags |= kfFilterAllReq;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8522
</td>
<td class="diff-line-num new_line" data-linenumber="8522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8522
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8522" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "gen-diff")) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8523
</td>
<td class="diff-line-num new_line" data-linenumber="8523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8523
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8523" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 7))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="8524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8524
</td>
<td class="diff-line-num new_line" data-linenumber="8524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8524
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8524" class="line" lang=""> goto main_ret_INVALID_CMDLINE_2A;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9328" style="width: 35px; color: rgba(0,0,0,0.3); 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="9328" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9328,16 +9328,16 @@ int main(int argc, char** argv) {</td>
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9328
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<td class="diff-line-num new_line" data-linenumber="9328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9328
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<pre style="margin: 0;"> <span id="LC9328" class="line" lang=""> const uint32_t mode_slen = strlen(mode_str);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9329
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<td class="diff-line-num new_line" data-linenumber="9329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9329
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<pre style="margin: 0;"> <span id="LC9329" class="line" lang=""> if (((mode_slen == 1) && (first_char_upcase_match == 'N')) ||</span>
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9330
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<td class="diff-line-num new_line" data-linenumber="9330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9330
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<pre style="margin: 0;"> <span id="LC9330" class="line" lang=""> strequal_k(mode_str, "natural", mode_slen)) {</span>
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<td class="diff-line-num old old_line" data-linenumber="9331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9331
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<td class="diff-line-num new_line old" data-linenumber="9331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9331" class="line" lang=""> pc.sort_vars_<span class="idiff left right">flags = kf</span>SortNatural;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="9332" style="width: 35px; color: rgba(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="9331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9331
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<pre style="margin: 0;">+<span id="LC9331" class="line" lang=""> pc.sort_vars_<span class="idiff left right">mode = k</span>SortNatural;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9332
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<td class="diff-line-num new_line" data-linenumber="9332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9332
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<pre style="margin: 0;"> <span id="LC9332" class="line" lang=""> } else if (likely(((mode_slen == 1) && (first_char_upcase_match == 'A')) ||</span>
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<td class="diff-line-num old_line" data-linenumber="9333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9333
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<td class="diff-line-num new_line" data-linenumber="9333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9333
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9333" class="line" lang=""> strequal_k(mode_str, "ascii", mode_slen))) {</span>
</pre>
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9334
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<td class="diff-line-num new_line old" data-linenumber="9334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9334" class="line" lang=""> pc.sort_vars_<span class="idiff left right">flags = kf</span>SortAscii;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="9335" style="width: 35px; color: rgba(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="9334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9334
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<pre style="margin: 0;">+<span id="LC9334" class="line" lang=""> pc.sort_vars_<span class="idiff left right">mode = k</span>SortAscii;</span>
</pre>
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9335
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<td class="diff-line-num new_line" data-linenumber="9335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9335
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<pre style="margin: 0;"> <span id="LC9335" class="line" lang=""> } else {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9336
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<td class="diff-line-num new_line" data-linenumber="9336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9336
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9336" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: '%s' is not a valid mode for --sort-vars.\n", mode_str);</span>
</pre>
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9337
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<td class="diff-line-num new_line" data-linenumber="9337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9337
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<pre style="margin: 0;"> <span id="LC9337" class="line" lang=""> goto main_ret_INVALID_CMDLINE_WWA;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9338
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<td class="diff-line-num new_line" data-linenumber="9338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9338
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<pre style="margin: 0;"> <span id="LC9338" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9339
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<td class="diff-line-num new_line" data-linenumber="9339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9339
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<pre style="margin: 0;"> <span id="LC9339" class="line" lang=""> } else {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9340
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<td class="diff-line-num new_line old" data-linenumber="9340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9340" class="line" lang=""> pc.sort_vars_<span class="idiff left right">flags = kf</span>SortNatural;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="9341" style="width: 35px; color: rgba(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="9340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9340
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<pre style="margin: 0;">+<span id="LC9340" class="line" lang=""> pc.sort_vars_<span class="idiff left right">mode = k</span>SortNatural;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9341
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<td class="diff-line-num new_line" data-linenumber="9341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9341
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<pre style="margin: 0;"> <span id="LC9341" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9342
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<td class="diff-line-num new_line" data-linenumber="9342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9342
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<pre style="margin: 0;"> <span id="LC9342" class="line" lang=""> } else if (strequal_k_unsafe(flagname_p2, "ample-diff")) {</span>
</pre>
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9343
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<td class="diff-line-num new_line" data-linenumber="9343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9343
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<pre style="margin: 0;"> <span id="LC9343" class="line" lang=""> if (unlikely(EnforceParamCtRange(argvk[arg_idx], param_ct, 1, 0x7fffffff))) {</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10303" style="width: 35px; color: rgba(0,0,0,0.3); 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="10303" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10303,7 +10303,7 @@ int main(int argc, char** argv) {</td>
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10303
</td>
<td class="diff-line-num new_line" data-linenumber="10303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10303
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10303" class="line" lang=""> logerrputs("Error: --data/--sample cannot be used with --1.\n");</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10304
</td>
<td class="diff-line-num new_line" data-linenumber="10304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10304
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10304" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10305
</td>
<td class="diff-line-num new_line" data-linenumber="10305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10305
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10305" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10306
</td>
<td class="diff-line-num new_line old" data-linenumber="10306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC10306" class="line" lang=""> if (unlikely((pc.sample_sort_<span class="idiff left right">flags != kf</span>Sort0) && (!(pc.command_flags1 & (kfCommand1MakePlink2 | kfCommand1WriteCovar | kfCommand1Pmerge))))) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10307" style="width: 35px; color: rgba(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="10306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10306
</td>
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<pre style="margin: 0;">+<span id="LC10306" class="line" lang=""> if (unlikely((pc.sample_sort_<span class="idiff left right">mode != k</span>Sort0) && (!(pc.command_flags1 & (kfCommand1MakePlink2 | kfCommand1WriteCovar | kfCommand1Pmerge))))) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10307
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<td class="diff-line-num new_line" data-linenumber="10307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10307
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10307" class="line" lang=""> logerrputs("Error: --indiv-sort must be used with --make-[b]pgen/--make-bed/--write-covar\nor dataset merging.\n");</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10308
</td>
<td class="diff-line-num new_line" data-linenumber="10308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10308
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10308" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10309
</td>
<td class="diff-line-num new_line" data-linenumber="10309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10309
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10309" class="line" lang=""> }</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10332" style="width: 35px; color: rgba(0,0,0,0.3); 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="10332" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10332,9 +10332,6 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10332
</td>
<td class="diff-line-num new_line" data-linenumber="10332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10332
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10332" class="line" lang=""> goto main_ret_INVALID_CMDLINE;</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="10333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10333
</td>
<td class="diff-line-num new_line" data-linenumber="10333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10333
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<pre style="margin: 0;"> <span id="LC10333" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10334
</td>
<td class="diff-line-num new_line" data-linenumber="10334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10334
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10334" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10335
</td>
<td class="diff-line-num new_line old" data-linenumber="10335" style="width: 35px; color: rgba(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="LC10335" class="line" lang=""> if ((pc.command_flags1 & kfCommand1Pmerge) && (pc.command_flags1 & (~kfCommand1Pmerge))) {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10336
</td>
<td class="diff-line-num new_line old" data-linenumber="10335" style="width: 35px; color: rgba(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="LC10336" class="line" lang=""> ;;;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10337
</td>
<td class="diff-line-num new_line old" data-linenumber="10335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10337" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10338
</td>
<td class="diff-line-num new_line" data-linenumber="10335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10335
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10335" class="line" lang=""> if (pc.keep_cat_phenoname && (!pc.keep_cat_names_flattened) && (!pc.keep_cats_fname)) {</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="10339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10339
</td>
<td class="diff-line-num new_line" data-linenumber="10336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10336
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10336" class="line" lang=""> logerrputs("Error: --keep-cat-pheno must be used with --keep-cats and/or --keep-cat-names.\n");</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10340
</td>
<td class="diff-line-num new_line" data-linenumber="10337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10337
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10337" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10529" style="width: 35px; color: rgba(0,0,0,0.3); 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="10526" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10529,10 +10526,10 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10529
</td>
<td class="diff-line-num new_line" data-linenumber="10526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10526
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10526" class="line" lang=""> // section; otherwise only do it in "--keep-autoconv vzs" case.</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="10530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10530
</td>
<td class="diff-line-num new_line" data-linenumber="10527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10527
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10527" class="line" lang=""> uint32_t pvar_is_compressed;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10531
</td>
<td class="diff-line-num new_line" data-linenumber="10528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10528
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10528" class="line" lang=""> if (xload & (kfXloadVcf | kfXloadBcf)) {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10532
</td>
<td class="diff-line-num new_line old" data-linenumber="10529" style="width: 35px; color: rgba(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="LC10532" class="line" lang=""> const uint32_t no_samples_ok = !(<span class="idiff left right">pc.dependency_flags & (kfFilterAllReq | kfFilterPsamReq</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="10533" style="width: 35px; color: rgba(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="10529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10529
</td>
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<pre style="margin: 0;">+<span id="LC10529" class="line" lang=""> const uint32_t no_samples_ok = !(<span class="idiff left right">(pc.dependency_flags & (kfFilterAllReq | kfFilterPsamReq)) || (pc.command_flags1 & kfCommand1Pmerge</span>));</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10533
</td>
<td class="diff-line-num new_line" data-linenumber="10530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10530
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10530" class="line" lang=""> const uint32_t is_vcf = (xload / kfXloadVcf) & 1;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10534
</td>
<td class="diff-line-num new_line" data-linenumber="10531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10531
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10531" class="line" lang=""> pvar_is_compressed = ((import_flags & (kfImportKeepAutoconv | kfImportKeepAutoconvVzs)) != kfImportKeepAutoconv);</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="10535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10535
</td>
<td class="diff-line-num new_line old" data-linenumber="10532" style="width: 35px; color: rgba(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="LC10535" class="line" lang=""> if (no_samples_ok && is_vcf && (!(import_flags & kfImportKeepAutoconv)) && pc.command_flags1<span class="idiff left right"> && (!(pc.command_flags1 & kfCommand1Pmerge))</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="10536" style="width: 35px; color: rgba(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="10532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10532
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10532" class="line" lang=""> if (no_samples_ok && is_vcf && (!(import_flags & kfImportKeepAutoconv)) && pc.command_flags1) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10536
</td>
<td class="diff-line-num new_line" data-linenumber="10533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10533
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10533" class="line" lang=""> // special case: just treat the VCF as a .pvar file</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10537
</td>
<td class="diff-line-num new_line" data-linenumber="10534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10534
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10534" class="line" lang=""> strcpy(pvarname, pgenname);</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="10538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10538
</td>
<td class="diff-line-num new_line" data-linenumber="10535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10535
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10535" class="line" lang=""> pgenname[0] = '\0';</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10608" style="width: 35px; color: rgba(0,0,0,0.3); 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="10605" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10608,7 +10605,12 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10608
</td>
<td class="diff-line-num new_line" data-linenumber="10605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10605
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10605" class="line" lang=""> if ((pc.dependency_flags & kfFilterOpportunisticPgen) && (pgenname[0] != '\0')) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10609
</td>
<td class="diff-line-num new_line" data-linenumber="10606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10606
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10606" class="line" lang=""> pc.dependency_flags |= kfFilterAllReq;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10610
</td>
<td class="diff-line-num new_line" data-linenumber="10607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10607
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10607" class="line" lang=""> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="10611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10611
</td>
<td class="diff-line-num new_line old" data-linenumber="10608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10611" class="line" lang=""> if (pc.dependency_flags & kfFilterAllReq) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10612" style="width: 35px; color: rgba(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="10608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10608
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10608" class="line" lang=""> if (pmerge_info.list_fname) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10612" style="width: 35px; color: rgba(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="10609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10609
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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="LC10609" class="line" lang=""> if (unlikely((!xload) && (load_params != kfLoadParamsPfileAll) && (load_params!= kfLoadParams0))) {</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10612" style="width: 35px; color: rgba(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="10610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10610
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<pre style="margin: 0;">+<span id="LC10610" class="line" lang=""> logerrputs("Error: --pmerge-list cannot be used with a proper subset of {--pgen, --pvar,\n--psam}. You must specify either none or all of those filenames.\n");</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10612" style="width: 35px; color: rgba(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="10611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10611
</td>
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<pre style="margin: 0;">+<span id="LC10611" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10612" style="width: 35px; color: rgba(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="10612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10612
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10612" class="line" lang=""> }</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="10612" style="width: 35px; color: rgba(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="10613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10613
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10613" class="line" lang=""> } else if ((pc.dependency_flags & kfFilterAllReq) || (pc.command_flags1 & kfCommand1Pmerge)) {</span>
</pre>
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</tr>
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<td class="diff-line-num old_line" data-linenumber="10612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10612
</td>
<td class="diff-line-num new_line" data-linenumber="10614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10614
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10614" class="line" lang=""> if (unlikely((!xload) && (load_params != kfLoadParamsPfileAll))) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10613
</td>
<td class="diff-line-num new_line" data-linenumber="10615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10615
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10615" class="line" lang=""> logerrputs("Error: A full fileset (.pgen/.bed + .pvar/.bim + .psam/.fam) is required for\nthis.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10614
</td>
<td class="diff-line-num new_line" data-linenumber="10616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10616
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10616" class="line" lang=""> goto main_ret_INVALID_CMDLINE_A;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10642" style="width: 35px; color: rgba(0,0,0,0.3); 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="10644" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10642,7 +10644,7 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10642
</td>
<td class="diff-line-num new_line" data-linenumber="10644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10644
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10644" class="line" lang=""> if (make_plink2_flags & (kfMakePgen | kfMakePvar | kfMakePsam)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10643
</td>
<td class="diff-line-num new_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">
10645
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10645" class="line" lang=""> merge_outname_end = strcpya_k(merge_outname_end, "-merge");</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10644
</td>
<td class="diff-line-num new_line" data-linenumber="10646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10646
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10646" class="line" lang=""> }</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="10645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10645
</td>
<td class="diff-line-num new_line old" data-linenumber="10647" style="width: 35px; color: rgba(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="LC10645" class="line" lang=""> reterr = Pmerge(&pmerge_info, pc.sample_sort_fname, pc.misc_flags, pc.sample_sort_<span class="idiff left right">flags</span>, pc.fam_cols, pc.max_thread_ct, pgenname, psamname, pvarname, outname, merge_outname_end, &chr_info);</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="10646" style="width: 35px; color: rgba(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="10647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10647
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10647" class="line" lang=""> reterr = Pmerge(&pmerge_info, pc.sample_sort_fname, pc.misc_flags, pc.sample_sort_<span class="idiff left right">mode</span>, pc.fam_cols, pc.max_thread_ct, pgenname, psamname, pvarname, outname, merge_outname_end, &chr_info);</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10646
</td>
<td class="diff-line-num new_line" data-linenumber="10648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10648
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10648" class="line" lang=""> if (unlikely(reterr)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10647
</td>
<td class="diff-line-num new_line" data-linenumber="10649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10649
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10649" class="line" lang=""> goto main_ret_1;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="10648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10648
</td>
<td class="diff-line-num new_line" data-linenumber="10650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10650
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10650" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10652" style="width: 35px; color: rgba(0,0,0,0.3); 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="10654" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10652,7 +10654,7 @@ int main(int argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10652
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<pre style="margin: 0;"> <span id="LC10654" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC10655" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC10656" class="line" lang=""></span>
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<pre style="margin: 0;">-<span id="LC10655" class="line" lang=""> if ((pc.command_flags1 & (~(kfCommand1MakePlink2 | kfCommand1Validate | kfCommand1WriteSnplist | kfCommand1WriteCovar | kfCommand1WriteSamples))) || ((pc.command_flags1 & kfCommand1MakePlink2) && (pc.sort_vars_<span class="idiff left right">flags == kfSort0</span>))) {</span>
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<pre style="margin: 0;">+<span id="LC10657" class="line" lang=""> if ((pc.command_flags1 & (~(kfCommand1MakePlink2 | kfCommand1Validate | kfCommand1WriteSnplist | kfCommand1WriteCovar | kfCommand1WriteSamples))) || ((pc.command_flags1 & kfCommand1MakePlink2) && (pc.sort_vars_<span class="idiff left right">mode > kSortNone</span>))) {</span>
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<pre style="margin: 0;"> <span id="LC10658" class="line" lang=""> // split-chromosome prohibited for all commands unless explicitly</span>
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<pre style="margin: 0;"> <span id="LC10659" class="line" lang=""> // permitted here</span>
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<pre style="margin: 0;"> <span id="LC10660" class="line" lang=""> pc.dependency_flags |= kfFilterNoSplitChr;</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1393,33 +1393,6 @@ BoolErr HtableGoodSizeAlloc(uint32_t item_ct, uintptr_t bytes_avail, uint32_t**</td>
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<pre style="margin: 0;"> <span id="LC1393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="cpp"></span>
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1396
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PopulateStrboxHtable</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">str_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_htable</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// may want subset_mask parameter later</span></span>
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1398
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">str_htable</span><span class="p">);</span></span>
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1399
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<pre style="margin: 0;">-<span id="LC1399" class="line" lang="cpp"> <span 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;">strbox_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strbox</span><span class="p">;</span></span>
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1400
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">str_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;">str_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">str_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">str_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">);</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// previously used quadratic probing, but turns out that that isn't</span></span>
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1403
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// meaningfully better than linear probing.</span></span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1405" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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1407
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="cpp"> <span class="n" style="color: #333;">str_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_idx</span><span class="p">;</span></span>
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1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1409
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strbox</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">]),</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// guaranteed to be positive</span></span>
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1412
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<pre style="margin: 0;">-<span id="LC1412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str_idx</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1413
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<td class="diff-line-num new_line old" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1414
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<pre style="margin: 0;">-<span id="LC1414" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1415
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1417
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1418
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="cpp"> <span class="n" style="color: #333;">strbox_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_str_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1419
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<pre style="margin: 0;">-<span id="LC1419" class="line" lang="cpp"> <span class="p">}</span></span>
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1420
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1421
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1422
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="cpp"></span>
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1423
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1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// could merge this with non-subset case, but this isn't much code</span></span>
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1424
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1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="diff-line-num old_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">uint32_t populate_strbox_subset_htable(const uintptr_t* __restrict subset_mask, const char* strbox, uintptr_t raw_str_ct, uintptr_t str_ct, uintptr_t max_str_blen, uint32_t str_htable_size, uint32_t* str_htable) {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); 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="1449" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1476,6 +1449,38 @@ uint32_t IdHtableFindNnt(const char* cur_id, const char* const* item_ids, const</td>
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1476
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1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1450" class="line" lang="cpp"><span class="p">}</span></span>
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1478
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1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="cpp"></span>
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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IdHtableAdd</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;">cur_id</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;">item_ids</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">)</span> <span class="p">{</span></span>
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1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="cpp"> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>
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1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="cpp"> <span class="p">}</span></span>
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1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">item_ids</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span><span class="p">],</span> <span class="n" style="color: #333;">cur_id_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="cpp"> <span class="p">}</span></span>
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1462
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<pre style="margin: 0;">+<span id="LC1462" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="cpp"> <span class="p">}</span></span>
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1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="cpp"> <span class="p">}</span></span>
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1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="cpp"><span class="p">}</span></span>
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1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="cpp"></span>
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1468
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<pre style="margin: 0;">+<span id="LC1468" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IdHtableAddNnt</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;">cur_id</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;">item_ids</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">)</span> <span class="p">{</span></span>
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1469
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<pre style="margin: 0;">+<span id="LC1469" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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1470
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<pre style="margin: 0;">+<span id="LC1470" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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1471
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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="cpp"> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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1473
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<pre style="margin: 0;">+<span id="LC1473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>
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1474
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<pre style="margin: 0;">+<span id="LC1474" class="line" lang="cpp"> <span class="p">}</span></span>
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1475
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<pre style="margin: 0;">+<span id="LC1475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">item_ids</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span><span class="p">],</span> <span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_id_slen</span><span class="p">))</span> <span class="p">{</span></span>
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1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="cpp"> <span class="p">}</span></span>
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1478
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<pre style="margin: 0;">+<span id="LC1478" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="cpp"> <span class="p">}</span></span>
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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="cpp"> <span class="p">}</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="cpp"><span class="p">}</span></span>
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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="cpp"></span>
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1479
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes cur_id_slen < max_str_blen.</span></span>
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1480
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// requires cur_id to be null-terminated.</span></span>
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1481
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrboxHtableFind</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;">cur_id</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;">strbox</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;">id_htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</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="1491" style="width: 35px; color: rgba(0,0,0,0.3); 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="1496" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1491,6 +1496,37 @@ uint32_t StrboxHtableFind(const char* cur_id, const char* strbox, const uint32_t</td>
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1491
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="cpp"> <span class="p">}</span></span>
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1492
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1497
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="cpp"><span class="p">}</span></span>
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1493
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1498
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<pre style="margin: 0;"> <span id="LC1498" class="line" lang="cpp"></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrboxHtableAdd</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;">cur_id</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">)</span> <span class="p">{</span></span>
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1500
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<pre style="margin: 0;">+<span id="LC1500" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1501
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<pre style="margin: 0;">+<span id="LC1501" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="cpp"> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>
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1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="cpp"> <span class="p">}</span></span>
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1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strbox</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">]),</span> <span class="n" style="color: #333;">cur_id_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="cpp"> <span class="p">}</span></span>
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1509
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<pre style="margin: 0;">+<span id="LC1509" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="cpp"> <span class="p">}</span></span>
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1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="cpp"> <span class="p">}</span></span>
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1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="cpp"><span class="p">}</span></span>
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1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="cpp"></span>
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1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PopulateStrboxHtable</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_htable</span><span class="p">)</span> <span class="p">{</span></span>
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1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// may want subset_mask parameter later</span></span>
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1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">str_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1518
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<pre style="margin: 0;">+<span id="LC1518" 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;">strbox_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strbox</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">str_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;">str_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">str_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">str_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">StrboxHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">,</span> <span class="n" style="color: #333;">strbox</span><span class="p">,</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">str_idx</span><span class="p">,</span> <span class="n" style="color: #333;">str_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// guaranteed to be positive</span></span>
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1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str_idx</span><span class="p">;</span></span>
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1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="cpp"> <span class="p">}</span></span>
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1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="cpp"> <span class="n" style="color: #333;">strbox_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strbox_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_str_blen</span><span class="p">]);</span></span>
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1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="cpp"> <span class="p">}</span></span>
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1527
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<pre style="margin: 0;">+<span id="LC1527" 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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1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="cpp"><span class="p">}</span></span>
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1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="cpp"></span>
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1494
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1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">VariantIdDupflagHtableFind</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;">idbuf</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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_id_slen</span><span class="p">)</span> <span class="p">{</span></span>
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1495
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assumes duplicate variant IDs are flagged, but full variant_uidx linked</span></span>
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1496
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1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// lists are not stored</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3071,7 +3107,6 @@ PglErr AllocAndPopulateIdHtableMt(const uintptr_t* subset_mask, const char* cons</td>
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3071
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3107
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<pre style="margin: 0;"> <span id="LC3107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">PopulateIdHtableMt</span><span class="p">(</span><span class="n" style="color: #333;">g_bigstack_end</span><span class="p">,</span> <span class="n" style="color: #333;">subset_mask</span><span class="p">,</span> <span class="n" style="color: #333;">item_ids</span><span class="p">,</span> <span class="n" style="color: #333;">item_ct</span><span class="p">,</span> <span class="n" style="color: #333;">store_all_dups</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g_bigstack_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id_htable_ptr</span><span class="p">,</span> <span class="n" style="color: #333;">dup_ct_ptr</span><span class="p">);</span></span>
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3072
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3108
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<pre style="margin: 0;"> <span id="LC3108" class="line" lang="cpp"><span class="p">}</span></span>
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3073
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3109
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<pre style="margin: 0;"> <span id="LC3109" class="line" lang="cpp"></span>
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3074
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<pre style="margin: 0;">-<span id="LC3074" class="line" lang="cpp"></span>
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3110
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<pre style="margin: 0;"> <span id="LC3110" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">Edit1Match</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;">s1</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;">s2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">len1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">len2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Permit one difference of the following forms (Damerau-Levenshtein distance</span></span>
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3112
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<pre style="margin: 0;"> <span id="LC3112" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1):</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#353424a9b88ab7aad403c3734bdd60f28af6b661"><strong>plink2_cmdline.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -957,10 +957,19 @@ HEADER_INLINE BoolErr arena_alloc_cp(unsigned char* arena_top, uintptr_t ct, uns</td>
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cp_arr_ptr</span><span class="p">);</span></span>
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="cpp"><span class="p">}</span></span>
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="cpp"></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">arena_alloc_kcp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_bottom_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;">kcp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kcp_arr_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="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="p">,</span> <span class="n" style="color: #333;">arena_alloc</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">),</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">));</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kcp_arr_ptr</span><span class="p">);</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"><span class="p">}</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"></span>
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960
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ArenaBaseSet</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">unaligned_base</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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961
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_bottom_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">unaligned_base</span><span class="p">),</span> <span class="n" style="color: #333;">kCacheline</span><span class="p">));</span></span>
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962
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"><span class="p">}</span></span>
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963
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ArenaEndSet</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">unaligned_end</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_top_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">RoundDownPow2</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">unaligned_end</span><span class="p">),</span> <span class="n" style="color: #333;">kEndAllocAlign</span><span class="p">));</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"><span class="p">}</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"></span>
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964
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_end_alloc_raw</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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965
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kEndAllocAlign</span><span class="p">));</span></span>
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966
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975
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<pre style="margin: 0;"> <span id="LC975" 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;">alloc_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_top_ptr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1028,6 +1037,11 @@ HEADER_INLINE BoolErr arena_end_alloc_cp(unsigned char* arena_bottom, uintptr_t</td>
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1028
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cp_arr_ptr</span><span class="p">);</span></span>
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1029
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="cpp"><span class="p">}</span></span>
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1030
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="cpp"></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">arena_end_alloc_kcp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_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;">kcp_arr_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kcp_arr_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="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="p">,</span> <span class="n" style="color: #333;">arena_end_alloc</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">),</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">));</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kcp_arr_ptr</span><span class="p">);</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"><span class="p">}</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"></span>
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1031
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1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="cpp"></span>
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1032
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">PushLlStr</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">LlStr</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">ll_stack_ptr</span><span class="p">);</span></span>
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1033
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1337" style="width: 35px; color: rgba(0,0,0,0.3); 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="1351" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1337,6 +1351,29 @@ HEADER_INLINE uint32_t Hashceil(const char* idstr, uint32_t idlen, uint32_t htab</td>
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1337
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span> <span class="n" style="color: #333;">Hash32</span><span class="p">(</span><span class="n" style="color: #333;">idstr</span><span class="p">,</span> <span class="n" style="color: #333;">idlen</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">htable_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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1338
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cpp"><span class="p">}</span></span>
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1339
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// In most cases, plink2 represents an array of strings in one of the following</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// two ways:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// (const char* strbox, uint32_t str_ct, uintptr_t max_str_blen):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// null-terminated string #x starts at &(strbox[x * max_str_blen)), where</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// x is a 0-based index.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// (const char* const* item_ids, uint32_t str_ct):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// null-terminated string #x starts at item_ids[x].</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// When we need to perform string -> string-index lookups into the array, we</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// construct a hashmap as follows:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Allocate a uint32_t array of htable_size >= 2 * str_ct, and initialize all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// entries to UINT32_MAX to mark them empty.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - Iterate through the array, computing hashval := Hashceil(str, strlen(str),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// htable_size) for each string, and then setting htable[hashval] :=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// string-index whenever that htable entry is empty. When there is a</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// conflict, use linear probing (increment hashval until an empty table cell</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// is found, wrapping around from (htable_size - 1) to 0).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// - PLINK 1.9 used quadratic probing, but that's been scrapped since</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// benchmark results suggest that it has no meaningful advantage. We</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// aren't dealing with adversarial input...</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The "StrboxHtable" functions below work with the const char* strbox</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// string-array representation, while "IdHtable" functions work with the const</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// char* const* item_ids representation.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"></span>
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1340
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<td class="diff-line-num new_line" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uintptr_t geqprime(uintptr_t floor);</span></span>
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1341
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1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"></span>
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1342
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1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes ceil is odd and greater than 4. Returns the first prime <= ceil.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); 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="1395" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1358,10 +1395,6 @@ HEADER_INLINE uint32_t GetHtableFastSize(uint32_t item_ct) {</td>
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1358
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1395
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1359
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<td class="diff-line-num new_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">HtableGoodSizeAlloc</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">item_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">bytes_avail</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">htable_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">htable_size_ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1360
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<td class="diff-line-num new_line" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="cpp"></span>
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1361
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<td class="diff-line-num new_line old" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1361" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// useful for duplicate detection: returns 0 on no duplicates, a positive index</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1362
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<td class="diff-line-num new_line old" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1362" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// of a duplicate pair if they're present</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1363
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<td class="diff-line-num new_line old" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1363" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PopulateStrboxHtable</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">str_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_htable</span><span class="p">);</span></span>
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1364
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<pre style="margin: 0;">-<span id="LC1364" class="line" lang="cpp"></span>
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1365
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1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// returned index in duplicate-pair case is unfiltered</span></span>
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<td class="diff-line-num old_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1366
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1399
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uint32_t populate_strbox_subset_htable(const uintptr_t* __restrict subset_mask, const char* strbox, uintptr_t raw_str_ct, uintptr_t str_ct, uintptr_t max_str_blen, uint32_t str_htable_size, uint32_t* str_htable);</span></span>
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1367
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1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1372,10 +1405,41 @@ uint32_t IdHtableFind(const char* cur_id, const char* const* item_ids, const uin</td>
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1372
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// null-terminated any more.</span></span>
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1373
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<td class="diff-line-num new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IdHtableFindNnt</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;">cur_id</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;">item_ids</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;">id_htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">);</span></span>
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1374
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1375" style="width: 35px; color: rgba(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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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HtableAddNondup</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;">cur_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1375" style="width: 35px; color: rgba(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="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="cpp"> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1414
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="cpp"> <span class="p">}</span></span>
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1415
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<pre style="margin: 0;">+<span id="LC1415" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">id_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"> <span class="p">}</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="cpp"> <span class="p">}</span></span>
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1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="cpp"><span class="p">}</span></span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="cpp"></span>
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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assumes cur_id is null-terminated.</span></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// item_ids overread must be ok.</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Returns string-index if cur_id is already in the table, UINT32_MAX if it was</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// added.</span></span>
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1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IdHtableAdd</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;">cur_id</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;">item_ids</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">);</span></span>
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1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="cpp"></span>
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1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Does not require cur_id to be null-terminated.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">IdHtableAddNnt</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;">cur_id</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;">item_ids</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">);</span></span>
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1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="cpp"></span>
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1375
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1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assumes cur_id_slen < max_str_blen.</span></span>
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1376
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1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// requires cur_id to be null-terminated.</span></span>
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1377
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1432
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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrboxHtableFind</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;">cur_id</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;">strbox</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;">id_htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">);</span></span>
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1378
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="cpp"></span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assumes cur_id is null-terminated.</span></span>
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1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Returns string-index if cur_id is already in the table, UINT32_MAX if it was</span></span>
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1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// added.</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrboxHtableAdd</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;">cur_id</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">);</span></span>
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1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cpp"></span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// useful for duplicate detection: returns 0 on no duplicates, a positive index</span></span>
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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// of a duplicate pair if they're present</span></span>
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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">PopulateStrboxHtable</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;">strbox</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_str_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_htable</span><span class="p">);</span></span>
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1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="cpp"></span>
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1379
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1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// last variant_ids entry must be at least kMaxIdBlen bytes before end of</span></span>
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1380
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// bigstack</span></span>
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1381
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">VariantIdDupflagHtableFind</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;">idbuf</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;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_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;">id_htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_id_slen</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); 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="1767" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1703,7 +1767,6 @@ PglErr CheckIdUniqueness(unsigned char* arena_bottom, unsigned char* arena_top,</td>
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<pre style="margin: 0;"> <span id="LC1767" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// not doing that again).</span></span>
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1768
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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">AllocAndPopulateIdHtableMt</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;">subset_mask</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;">item_ids</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">item_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">fast_size_min_extra_bytes</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;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">id_htable_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">htable_dup_base_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">id_htable_size_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dup_ct_ptr</span><span class="p">);</span></span>
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1705
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1769
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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="cpp"></span>
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1706
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<pre style="margin: 0;">-<span id="LC1706" class="line" lang="cpp"></span>
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1707
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1770
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<pre style="margin: 0;"> <span id="LC1770" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">HelpCtrlStruct</span> <span class="p">{</span></span>
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1708
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1771
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<pre style="margin: 0;"> <span id="LC1771" class="line" lang="cpp"> <span class="n" style="color: #333;">NONCOPYABLE</span><span class="p">(</span><span class="n" style="color: #333;">HelpCtrlStruct</span><span class="p">);</span></span>
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1709
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1772
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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">iters_left</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); 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="1794" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1794,15 +1794,8 @@ PglErr TryToAddChrName(const char* chr_name, const char* file_descrip, uintptr_t</td>
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1794
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1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chr_idx_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chr_code_end</span><span class="p">;</span></span>
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1795
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1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="cpp"> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1796
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1796
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<pre style="margin: 0;"> <span id="LC1796" 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;">id_htable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nonstd_id_htable</span><span class="p">;</span></span>
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1797
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<td class="diff-line-num new_line old" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1797" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">chr_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_slen</span><span class="p">,</span> <span class="n" style="color: #333;">kChrHtableSize</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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1798
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<pre style="margin: 0;">-<span id="LC1798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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1799
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<td class="diff-line-num new_line old" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1799" class="line" lang="cpp"> <span class="n" style="color: #333;">id_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chr_code_end</span><span class="p">;</span></span>
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1800
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<pre style="margin: 0;">-<span id="LC1800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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1801
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<pre style="margin: 0;">-<span id="LC1801" class="line" lang="cpp"> <span class="p">}</span></span>
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1802
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<pre style="margin: 0;">-<span id="LC1802" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kChrHtableSize</span><span class="p">)</span> <span class="p">{</span></span>
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1803
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<pre style="margin: 0;">-<span id="LC1803" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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1804
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<pre style="margin: 0;">-<span id="LC1804" class="line" lang="cpp"> <span class="p">}</span></span>
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1805
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<pre style="margin: 0;">-<span id="LC1805" class="line" lang="cpp"> <span class="p">}</span></span>
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1797
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<pre style="margin: 0;">+<span id="LC1797" class="line" lang="cpp"> <span class="n" style="color: #333;">HtableAddNondup</span><span class="p">(</span><span class="n" style="color: #333;">chr_name</span><span class="p">,</span> <span class="n" style="color: #333;">name_slen</span><span class="p">,</span> <span class="n" style="color: #333;">kChrHtableSize</span><span class="p">,</span> <span class="n" style="color: #333;">chr_code_end</span><span class="p">,</span> <span class="n" style="color: #333;">id_htable</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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1806
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1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="cpp"><span class="p">}</span></span>
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1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="cpp"></span>
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1801
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<pre style="margin: 0;"> <span id="LC1801" 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">@@ -3037,6 +3030,115 @@ void ExpandMhc(uint32_t sample_ct, uintptr_t* mhc, uintptr_t** patch_01_set_ptr,</td>
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3037
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3030
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<pre style="margin: 0;"> <span id="LC3030" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">patch_10_vals_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</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;">patch_10_set</span><span class="p">[</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">]));</span></span>
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3038
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3031
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<pre style="margin: 0;"> <span id="LC3031" class="line" lang="cpp"><span class="p">}</span></span>
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3039
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3032
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<pre style="margin: 0;"> <span id="LC3032" class="line" lang="cpp"></span>
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3033
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<pre style="margin: 0;">+<span id="LC3033" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Returns 2 if resize needed (str_ct == strset_table_size / 2), 1 if OOM</span></span>
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3034
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<pre style="margin: 0;">+<span id="LC3034" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrsetAdd</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size</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;">strset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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3035
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<pre style="margin: 0;">+<span id="LC3035" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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3036
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<pre style="margin: 0;">+<span id="LC3036" 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;">strset_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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3037
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<pre style="margin: 0;">+<span id="LC3037" 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;">strset_entry</span><span class="p">)</span> <span class="p">{</span></span>
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3038
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<pre style="margin: 0;">+<span id="LC3038" 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;">str_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span><span class="p">);</span></span>
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3039
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<pre style="margin: 0;">+<span id="LC3039" 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;">str_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">))</span> <span class="p">{</span></span>
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3040
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<pre style="margin: 0;">+<span id="LC3040" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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3041
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<pre style="margin: 0;">+<span id="LC3041" class="line" lang="cpp"> <span class="p">}</span></span>
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3042
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<pre style="margin: 0;">+<span id="LC3042" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_ct</span><span class="p">;</span></span>
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3043
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<pre style="margin: 0;">+<span id="LC3043" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="n" style="color: #333;">StoreStringAtBase</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">])));</span></span>
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<pre style="margin: 0;">+<span id="LC3044" class="line" lang="cpp"> <span class="p">}</span></span>
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3045
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<pre style="margin: 0;">+<span id="LC3045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">strset_entry</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">))</span> <span class="p">{</span></span>
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3046
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<pre style="margin: 0;">+<span id="LC3046" 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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3047
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<pre style="margin: 0;">+<span id="LC3047" class="line" lang="cpp"> <span class="p">}</span></span>
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3048
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<pre style="margin: 0;">+<span id="LC3048" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">)</span> <span class="p">{</span></span>
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3049
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<pre style="margin: 0;">+<span id="LC3049" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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3050
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<pre style="margin: 0;">+<span id="LC3050" class="line" lang="cpp"> <span class="p">}</span></span>
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3051
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<pre style="margin: 0;">+<span id="LC3051" class="line" lang="cpp"> <span class="p">}</span></span>
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3052
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<pre style="margin: 0;">+<span id="LC3052" class="line" lang="cpp"><span class="p">}</span></span>
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3053
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<pre style="margin: 0;">+<span id="LC3053" class="line" lang="cpp"></span>
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3054
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<pre style="margin: 0;">+<span id="LC3054" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">StrsetAddEnd</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size</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;">strset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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3055
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<pre style="margin: 0;">+<span id="LC3055" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3056
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<pre style="margin: 0;">+<span id="LC3056" 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;">strset_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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3057
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<pre style="margin: 0;">+<span id="LC3057" 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;">strset_entry</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3058
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<pre style="margin: 0;">+<span id="LC3058" 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;">str_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3059
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<pre style="margin: 0;">+<span id="LC3059" 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;">str_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3060
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3062
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<pre style="margin: 0;">+<span id="LC3062" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3063
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<pre style="margin: 0;">+<span id="LC3063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="n" style="color: #333;">StoreStringAtEnd</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</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="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">strset_entry</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">))</span> <span class="p">{</span></span>
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3066
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<pre style="margin: 0;">+<span id="LC3066" 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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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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3068
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<pre style="margin: 0;">+<span id="LC3068" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">)</span> <span class="p">{</span></span>
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3069
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<pre style="margin: 0;">+<span id="LC3069" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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3070
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<pre style="margin: 0;">+<span id="LC3070" class="line" lang="cpp"> <span class="p">}</span></span>
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3071
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<pre style="margin: 0;">+<span id="LC3071" class="line" lang="cpp"> <span class="p">}</span></span>
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3072
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<pre style="margin: 0;">+<span id="LC3072" class="line" lang="cpp"><span class="p">}</span></span>
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3073
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<pre style="margin: 0;">+<span id="LC3073" class="line" lang="cpp"></span>
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3074
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<pre style="margin: 0;">+<span id="LC3074" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RepopulateStrset</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;">str_iter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">str_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_size</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;">strset</span><span class="p">)</span> <span class="p">{</span></span>
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3075
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<pre style="margin: 0;">+<span id="LC3075" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroPtrArr</span><span class="p">(</span><span class="n" style="color: #333;">strset_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3076
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<pre style="margin: 0;">+<span id="LC3076" 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;">str_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;">str_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">str_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">str_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3077
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<pre style="margin: 0;">+<span id="LC3077" 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;">str_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strnul</span><span class="p">(</span><span class="n" style="color: #333;">str_iter</span><span class="p">);</span></span>
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3078
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<pre style="margin: 0;">+<span id="LC3078" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">str_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3079
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<pre style="margin: 0;">+<span id="LC3079" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">str_iter</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">strset_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3080
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<pre style="margin: 0;">+<span id="LC3080" 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;">strset_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3081
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<pre style="margin: 0;">+<span id="LC3081" 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;">strset_entry</span><span class="p">)</span> <span class="p">{</span></span>
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3082
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<pre style="margin: 0;">+<span id="LC3082" class="line" lang="cpp"> <span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str_iter</span><span class="p">;</span></span>
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3083
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<pre style="margin: 0;">+<span id="LC3083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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3084
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<pre style="margin: 0;">+<span id="LC3084" class="line" lang="cpp"> <span class="p">}</span></span>
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3085
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<pre style="margin: 0;">+<span id="LC3085" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strset_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3086
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<pre style="margin: 0;">+<span id="LC3086" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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3087
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<pre style="margin: 0;">+<span id="LC3087" class="line" lang="cpp"> <span class="p">}</span></span>
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3088
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<pre style="margin: 0;">+<span id="LC3088" class="line" lang="cpp"> <span class="p">}</span></span>
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3089
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<pre style="margin: 0;">+<span id="LC3089" class="line" lang="cpp"> <span class="n" style="color: #333;">str_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">str_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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3090
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<pre style="margin: 0;">+<span id="LC3090" class="line" lang="cpp"> <span class="p">}</span></span>
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3091
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<pre style="margin: 0;">+<span id="LC3091" class="line" lang="cpp"><span class="p">}</span></span>
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3092
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<pre style="margin: 0;">+<span id="LC3092" class="line" lang="cpp"></span>
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3093
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<pre style="margin: 0;">+<span id="LC3093" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">StrsetAddResize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size_max</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;">strset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strset_table_sizep</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3094
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<pre style="margin: 0;">+<span id="LC3094" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strset_table_sizep</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3095
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<pre style="margin: 0;">+<span id="LC3095" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StrsetAdd</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">,</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3096
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<pre style="margin: 0;">+<span id="LC3096" 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;">retval</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3097
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<pre style="margin: 0;">+<span id="LC3097" 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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3098
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<pre style="margin: 0;">+<span id="LC3098" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3099
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<pre style="margin: 0;">+<span id="LC3099" 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;">retval</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strset_table_size_max</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3100
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<pre style="margin: 0;">+<span id="LC3100" 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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3101
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<pre style="margin: 0;">+<span id="LC3101" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3102
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<pre style="margin: 0;">+<span id="LC3102" 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_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MINV</span><span class="p">(</span><span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2LLU</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size_max</span><span class="p">);</span></span>
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3103
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<pre style="margin: 0;">+<span id="LC3103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bytes_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">new_table_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3104
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<pre style="margin: 0;">+<span id="LC3104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bytes_needed</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3105
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<pre style="margin: 0;">+<span id="LC3105" 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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3106
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<pre style="margin: 0;">+<span id="LC3106" class="line" lang="cpp"> <span class="p">}</span></span>
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3107
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<pre style="margin: 0;">+<span id="LC3107" 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;">old_str_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">strset_table_size</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3108
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<pre style="margin: 0;">+<span id="LC3108" 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;">new_str_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">strset</span><span class="p">[</span><span class="n" style="color: #333;">new_table_size</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3109
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<pre style="margin: 0;">+<span id="LC3109" class="line" lang="cpp"> <span class="n" style="color: #333;">memmove</span><span class="p">(</span><span class="n" style="color: #333;">new_str_base</span><span class="p">,</span> <span class="n" style="color: #333;">old_str_base</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">old_str_base</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3110
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<pre style="margin: 0;">+<span id="LC3110" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_bottom_ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bytes_needed</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3111
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<pre style="margin: 0;">+<span id="LC3111" class="line" lang="cpp"> <span class="n" style="color: #333;">RepopulateStrset</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">new_str_base</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3112
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<pre style="margin: 0;">+<span id="LC3112" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strset_table_sizep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3113
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<pre style="margin: 0;">+<span id="LC3113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">StrsetAdd</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">,</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">arena_bottom_ptr</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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3114
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<pre style="margin: 0;">+<span id="LC3114" class="line" lang="cpp"><span class="p">}</span></span>
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3115
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<pre style="margin: 0;">+<span id="LC3115" class="line" lang="cpp"></span>
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3116
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<pre style="margin: 0;">+<span id="LC3116" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">StrsetAddEndResize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size_max</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;">strsetp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strset_table_sizep</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3117
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<pre style="margin: 0;">+<span id="LC3117" 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;">strset</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strsetp</span><span class="p">;</span></span>
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3118
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<pre style="margin: 0;">+<span id="LC3118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strset_table_sizep</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3119
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<pre style="margin: 0;">+<span id="LC3119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StrsetAddEnd</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">,</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">);</span></span>
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3120
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<pre style="margin: 0;">+<span id="LC3120" 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;">retval</span><span class="p">)</span> <span class="p">{</span></span>
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3121
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<pre style="margin: 0;">+<span id="LC3121" 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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3122
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<pre style="margin: 0;">+<span id="LC3122" class="line" lang="cpp"> <span class="p">}</span></span>
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3123
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<pre style="margin: 0;">+<span id="LC3123" 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;">retval</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">strset_table_size_max</span><span class="p">)))</span> <span class="p">{</span></span>
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3124
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<pre style="margin: 0;">+<span id="LC3124" 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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3125
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<pre style="margin: 0;">+<span id="LC3125" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3126
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<pre style="margin: 0;">+<span id="LC3126" 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_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MINV</span><span class="p">(</span><span class="n" style="color: #333;">strset_table_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2LLU</span><span class="p">,</span> <span class="n" style="color: #333;">strset_table_size_max</span><span class="p">);</span></span>
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3127
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<pre style="margin: 0;">+<span id="LC3127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bytes_needed</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">new_table_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3128
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<pre style="margin: 0;">+<span id="LC3128" 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;">old_str_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_top_ptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3129
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<pre style="margin: 0;">+<span id="LC3129" 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;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">old_str_base</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bytes_needed</span><span class="p">))</span> <span class="p">{</span></span>
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3130
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<pre style="margin: 0;">+<span id="LC3130" 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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3131
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<pre style="margin: 0;">+<span id="LC3131" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3132
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<pre style="margin: 0;">+<span id="LC3132" 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;">new_str_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_str_base</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bytes_needed</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3133
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<pre style="margin: 0;">+<span id="LC3133" class="line" lang="cpp"> <span class="n" style="color: #333;">memmove</span><span class="p">(</span><span class="n" style="color: #333;">new_str_base</span><span class="p">,</span> <span class="n" style="color: #333;">old_str_base</span><span class="p">,</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">old_str_base</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3134
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<pre style="margin: 0;">+<span id="LC3134" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">arena_top_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_str_base</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3135
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<pre style="margin: 0;">+<span id="LC3135" class="line" lang="cpp"> <span class="n" style="color: #333;">strset</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">new_table_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strset_table_size</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3136
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<pre style="margin: 0;">+<span id="LC3136" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strsetp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strset</span><span class="p">;</span></span>
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3137
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<pre style="margin: 0;">+<span id="LC3137" class="line" lang="cpp"> <span class="n" style="color: #333;">RepopulateStrset</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">new_str_base</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3138
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<pre style="margin: 0;">+<span id="LC3138" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">strset_table_sizep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">;</span></span>
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3139
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<pre style="margin: 0;">+<span id="LC3139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">StrsetAddEnd</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">new_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">strset</span><span class="p">,</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</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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3140
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<pre style="margin: 0;">+<span id="LC3140" class="line" lang="cpp"><span class="p">}</span></span>
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3141
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<pre style="margin: 0;">+<span id="LC3141" class="line" lang="cpp"></span>
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3040
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3142
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<pre style="margin: 0;"> <span id="LC3142" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteSampleIdsOverride</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">SampleIdFlags</span> <span class="n" style="color: #333;">override_flags</span><span class="p">)</span> <span class="p">{</span></span>
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3041
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3143
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<pre style="margin: 0;"> <span id="LC3143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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3042
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3144
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<pre style="margin: 0;"> <span id="LC3144" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#576e4fd14d1d66b779bb9f5d05d29f2871392d1a"><strong>plink2_common.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -226,6 +226,7 @@ FLAGSET_DEF_START()</td>
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226
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">kfPsamColAll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">kfPsamColPhenos</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kfPsamColMaybefid</span><span class="p">)</span></span>
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227
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">PvarPsamFlags</span><span class="p">);</span></span>
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228
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// may want to rename FidPresent to FidMayBePresent</span></span>
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229
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_START</span><span class="p">()</span></span>
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230
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSampleId0</span><span class="p">,</span></span>
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231
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSampleIdFidPresent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -985,6 +986,8 @@ typedef struct PhenoColStruct {</td>
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985
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986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// * When .sample non-V2 categorical variables are imported, 'C' is added in</span></span>
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986
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// front of the integers.</span></span>
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987
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988
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// * category_names[1..(n-1)] is guaranteed to be in natural-sorted order.</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (MergePsams() has slightly different behavior since its pheno_cols</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// instance is only used for a one-time internal write.)</span></span>
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988
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991
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<pre style="margin: 0;"> <span id="LC991" 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;">category_names</span><span class="p">;</span></span>
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989
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp"></span>
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990
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<pre style="margin: 0;"> <span id="LC993" 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;">nonmiss</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// bitvector</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1109,8 +1112,25 @@ HEADER_INLINE BoolErr StoreStringAndPrecharAtEnd(unsigned char* arena_bottom, co</td>
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1109
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1112
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<pre style="margin: 0;"> <span id="LC1112" 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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1110
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp"><span class="p">}</span></span>
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1111
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Memory layout:</span></span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// [ strset ][packed strings]</span></span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ^</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// |</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// arena_bottom</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// strset pointers do not remain valid after resize.</span></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="cpp"></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// returns 1 if resize needed, 2 if OOM</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uint32_t StrsetAdd(unsigned char* arena_top, const char* src, uint32_t slen, uint32_t strset_table_size, char** strset, uint32_t* str_ctp, unsigned char** arena_bottom_ptr);</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// uint32_t StrsetAddEnd(unsigned char* arena_bottom, const char* src, uint32_t slen, uint32_t strset_table_size, char** strset, uint32_t* str_ctp, unsigned char** arena_top_ptr);</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">StrsetAddResize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size_max</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;">strset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strset_table_sizep</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_bottom_ptr</span><span class="p">);</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">StrsetAddEndResize</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">strset_table_size_max</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;">strsetp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strset_table_sizep</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">str_ctp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"></span>
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1112
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// These use g_textbuf.</span></span>
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteSampleIdsOverride</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">SampleIdFlags</span> <span class="n" style="color: #333;">override_flags</span><span class="p">);</span></span>
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1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cpp"></span>
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1114
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="cpp"><span class="n" style="color: #333;">HEADER_INLINE</span> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteSampleIds</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">)</span> <span class="p">{</span></span>
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1115
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">WriteSampleIdsOverride</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">siip</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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1116
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -928,17 +928,17 @@ uint32_t DataSidColIsRequired(const uintptr_t* sample_include, const char* sids,</td>
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<pre style="margin: 0;"> <span id="LC928" 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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929
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"><span class="p">}</span></span>
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">PedigreeIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pii</span>p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">SampleIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">siip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ParentalIdInfo</span></span><span 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">parental_id_info</span>p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">)</span> <span class="p">{</span></span>
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932
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maybe_modifier</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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933
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933
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<pre style="margin: 0;"> <span id="LC933" 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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934
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp"> <span class="p">}</span></span>
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935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">maybe_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfSampleIdParentsPresent</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">maybe_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfSampleIdParentsPresent</span><span class="p">)))</span> <span class="p">{</span></span>
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936
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<pre style="margin: 0;"> <span id="LC936" 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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937
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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="cpp"> <span class="p">}</span></span>
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938
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<pre style="margin: 0;">-<span id="LC938" 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;">paternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">paternal_ids</span><span class="p">;</span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" 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;">maternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">maternal_ids</span><span class="p">;</span></span>
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940
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" 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;">paternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">paternal_ids</span><span class="p">;</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" 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;">maternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">maternal_ids</span><span class="p">;</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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942
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">sample_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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943
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_include</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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944
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -966,29 +966,28 @@ char* AppendPhenoStr(const PhenoCol* pheno_col, const char* output_missing_pheno</td>
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966
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">write_iter</span><span class="p">;</span></span>
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"><span class="p">}</span></span>
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968
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePsam</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">PedigreeIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_sample_idx_to_old</span></span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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="n" style="color: #333;">PvarPsamFlags</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">)</span> <span class="p">{</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePsam</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">SampleIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">siip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ParentalIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parental_id_infop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uintptr_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PhenoCol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint32_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">output_missing_pheno</span></span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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="n" style="color: #333;">PvarPsamFlags</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">)</span> <span class="p">{</span></span>
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970
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
971
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
972
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
973
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<td class="diff-line-num new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
973
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<pre style="margin: 0;"> <span id="LC973" 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;">fopen_checked</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">FOPEN_WB</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">outfile</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
974
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WritePsam_ret_OPEN_FAIL</span><span class="p">;</span></span>
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975
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"> <span class="p">}</span></span>
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976
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<td class="diff-line-num new_line old" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_missing_pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_output_missing_pheno</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
977
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">omp_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">output_missing_pheno</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
978
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="cpp"></span>
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979
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978
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<pre style="margin: 0;"> <span id="LC978" 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;">textbuf_flush</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_textbuf</span><span class="p">[</span><span class="n" style="color: #333;">kMaxMediumLine</span><span class="p">]);</span></span>
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980
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="cpp"></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">sids</span><span class="p">;</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" 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;">paternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">paternal_ids</span><span class="p">;</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" 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;">maternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">maternal_ids</span><span class="p">;</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">;</span></span>
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987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">iip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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989
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_fid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataFidColIsRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColMaybefid</span><span class="p">);</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">sids</span><span class="p">;</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" 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;">paternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">paternal_ids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
983
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<pre style="margin: 0;">+<span id="LC983" 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;">maternal_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">maternal_ids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">;</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p<span class="idiff left">arental_id_infop</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_fid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataFidColIsRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">siip</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColMaybefid</span><span class="p">);</span></span>
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990
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989
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_sid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataSidColIsRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColMaybesid</span><span class="p">);</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">pii</span>p</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColMaybeparents</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">siip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">parental_id_info</span>p</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColMaybeparents</span><span class="p">);</span></span>
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992
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_sex</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfPsamColSex</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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993
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_empty_pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPsamColPheno1</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;">pheno_ct</span><span class="p">);</span></span>
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994
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_phenos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pvar_psam_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">kfPsamColPheno1</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfPsamColPhenos</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4184" style="width: 35px; color: rgba(0,0,0,0.3); 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="4183" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4184,6 +4183,7 @@ PglErr MakeFilterHtable(const uintptr_t* variant_include, const uintptr_t* filte</td>
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4184
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4183
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<pre style="margin: 0;"> <span id="LC4183" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// while still being small relative to L1 cache. Double table size</span></span>
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<td class="diff-line-num old_line" data-linenumber="4185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4185
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4184
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<pre style="margin: 0;"> <span id="LC4184" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// whenever load factor reaches 0.25; there shouldn't be *that* many</span></span>
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4186
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4185
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<pre style="margin: 0;"> <span id="LC4185" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// distinct filters.</span></span>
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4186
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<pre style="margin: 0;">+<span id="LC4186" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: check if this should use strset instead</span></span>
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4187
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4187
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<pre style="margin: 0;"> <span id="LC4187" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// possible todo: multithread this scan, merge results at the end; can also</span></span>
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4188
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4188
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<pre style="margin: 0;"> <span id="LC4188" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// separate this stage from the rest of the function.</span></span>
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4189
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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;">uint32_t</span> <span class="n" style="color: #333;">table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">128</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4254" style="width: 35px; color: rgba(0,0,0,0.3); 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="4254" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4254,7 +4254,7 @@ PglErr MakeFilterHtable(const uintptr_t* variant_include, const uintptr_t* filte</td>
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4254
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4254
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<pre style="margin: 0;"> <span id="LC4254" class="line" lang="cpp"> <span class="p">}</span></span>
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4255
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4255
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<pre style="margin: 0;"> <span id="LC4255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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4256
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4256
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<pre style="margin: 0;"> <span id="LC4256" class="line" lang="cpp"> <span class="p">}</span></span>
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4257
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<pre style="margin: 0;">-<span id="LC4257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">memcmp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filter_iter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cur_token_ptr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cur_id_slen</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="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">cur_token_ptr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">cur_id_slen</span></span><span class="p"><span class="idiff right">]</span>))</span> <span class="p">{</span></span>
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4257
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<pre style="margin: 0;">+<span id="LC4257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">strequal_unsafe</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filter_iter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cur_token_ptr</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_id_slen</span></span><span class="p">))</span> <span class="p">{</span></span>
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4258
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4258
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<pre style="margin: 0;"> <span id="LC4258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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4259
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4259
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<pre style="margin: 0;"> <span id="LC4259" class="line" lang="cpp"> <span class="p">}</span></span>
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4260
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4260
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<pre style="margin: 0;"> <span id="LC4260" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_size</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="4292" style="width: 35px; color: rgba(0,0,0,0.3); 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="4292" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4292,14 +4292,7 @@ PglErr MakeFilterHtable(const uintptr_t* variant_include, const uintptr_t* filte</td>
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4292
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4292
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<pre style="margin: 0;"> <span id="LC4292" 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;">filter_keys_htable</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filter_keys_htable_ptr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4293
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4293
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<pre style="margin: 0;"> <span id="LC4293" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">filter_keys_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">filter_keys_htable</span><span class="p">);</span></span>
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4294
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4294
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<pre style="margin: 0;"> <span id="LC4294" 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;">filter_key_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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4295
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<td class="diff-line-num new_line old" data-linenumber="4295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4295" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">filter_keys</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">],</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">filter_keys</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">]),</span> <span class="n" style="color: #333;">filter_keys_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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4296
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<td class="diff-line-num new_line old" data-linenumber="4295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter_keys_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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4297
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<pre style="margin: 0;">-<span id="LC4297" class="line" lang="cpp"> <span class="n" style="color: #333;">filter_keys_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</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>
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4298
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<pre style="margin: 0;">-<span id="LC4298" class="line" lang="cpp"> <span class="p">}</span></span>
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4299
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<pre style="margin: 0;">-<span id="LC4299" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">filter_keys_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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4300
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<pre style="margin: 0;">-<span id="LC4300" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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4301
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<pre style="margin: 0;">-<span id="LC4301" class="line" lang="cpp"> <span class="p">}</span></span>
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4302
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<pre style="margin: 0;">-<span id="LC4302" class="line" lang="cpp"> <span class="p">}</span></span>
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4295
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<pre style="margin: 0;">+<span id="LC4295" class="line" lang="cpp"> <span class="n" style="color: #333;">HtableAddNondup</span><span class="p">(</span><span class="n" style="color: #333;">filter_keys</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">],</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">filter_keys</span><span class="p">[</span><span class="n" style="color: #333;">uii</span><span class="p">]),</span> <span class="n" style="color: #333;">filter_keys_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">uii</span><span class="p">,</span> <span class="n" style="color: #333;">filter_keys_htable</span><span class="p">);</span></span>
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4303
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4296
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<pre style="margin: 0;"> <span id="LC4296" class="line" lang="cpp"> <span class="p">}</span></span>
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4304
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4297
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<pre style="margin: 0;"> <span id="LC4297" class="line" lang="cpp"> <span class="p">}</span></span>
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4305
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<td class="diff-line-num new_line" data-linenumber="4298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4298
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<pre style="margin: 0;"> <span id="LC4298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6758" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6765,7 +6758,7 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*</td>
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6765
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<td class="diff-line-num new_line" data-linenumber="6758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6758
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<pre style="margin: 0;"> <span id="LC6758" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span><span class="p">,</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6766
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<td class="diff-line-num new_line" data-linenumber="6759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6759
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<pre style="margin: 0;"> <span id="LC6759" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintfww5</span><span class="p">(</span><span class="s" style="color: #d14;">"Writing %s ... "</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="6767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6767
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<td class="diff-line-num new_line" data-linenumber="6760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6760
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<pre style="margin: 0;"> <span id="LC6760" class="line" lang="cpp"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6768
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<td class="diff-line-num new_line old" data-linenumber="6761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6768" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WritePsam</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_sample_idx_to_old</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6769" style="width: 35px; color: rgba(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="6761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6761
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<pre style="margin: 0;">+<span id="LC6761" 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;">WritePsam</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</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="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g_output_missing_pheno</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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6769
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<td class="diff-line-num new_line" data-linenumber="6762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6762
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<pre style="margin: 0;"> <span id="LC6762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6770
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<td class="diff-line-num new_line" data-linenumber="6763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6763
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<pre style="margin: 0;"> <span id="LC6763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2NoVsort_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6771
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<td class="diff-line-num new_line" data-linenumber="6764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6764
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<pre style="margin: 0;"> <span id="LC6764" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8218" style="width: 35px; color: rgba(0,0,0,0.3); 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="8211" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -8218,7 +8211,7 @@ PglErr MakePlink2Vsort(const uintptr_t* sample_include, const PedigreeIdInfo* pi</td>
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<td class="diff-line-num old_line" data-linenumber="8218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8218
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<td class="diff-line-num new_line" data-linenumber="8211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8211
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<pre style="margin: 0;"> <span id="LC8211" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span><span class="p">,</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="8219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8219
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<td class="diff-line-num new_line" data-linenumber="8212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8212
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<pre style="margin: 0;"> <span id="LC8212" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintfww5</span><span class="p">(</span><span class="s" style="color: #d14;">"Writing %s ... "</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="8220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8220
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<td class="diff-line-num new_line" data-linenumber="8213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8213
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<pre style="margin: 0;"> <span id="LC8213" class="line" lang="cpp"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8221
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<td class="diff-line-num new_line old" data-linenumber="8214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8221" 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;">WritePsam</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">piip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_sample_idx_to_old</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="8222" style="width: 35px; color: rgba(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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8214
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<pre style="margin: 0;">+<span id="LC8214" 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;">WritePsam</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</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="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_nm</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sex_male</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_cols</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pheno_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_sample_idx_to_old</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g_output_missing_pheno</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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8222
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8215
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<pre style="margin: 0;"> <span id="LC8215" 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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8223
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8216
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<pre style="margin: 0;"> <span id="LC8216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MakePlink2Vsort_ret_1</span><span class="p">;</span></span>
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8224
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8217
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<pre style="margin: 0;"> <span id="LC8217" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#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">@@ -63,6 +63,8 @@ CONSTI32(kMaxInfoKeySlen, kMaxIdSlen);</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WriteMapOrBim</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_presents</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">STD_ARRAY_PTR_DECL</span><span class="p">(</span><span class="n" style="color: #333;">AlleleCode</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">refalt1_select</span><span class="p">),</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_cms</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">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;">char</span> <span class="n" style="color: #333;">delim</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>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">WritePsam</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">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="n" style="color: #333;">ParentalIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parental_id_infop</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_missing_pheno</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">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="n" style="color: #333;">PvarPsamFlags</span> <span class="n" style="color: #333;">pvar_psam_flags</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarInfoOpenAndReloadHeader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_info_reload</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">TextStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_reload_txsp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">line_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">info_col_idx_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PvarInfoReload</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">info_col_idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_uidx</span><span class="p">,</span> <span class="n" style="color: #333;">TextStream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_reload_txsp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">line_iterp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">trs_variant_uidx_ptr</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,7 +85,7 @@ uint32_t DataFidColIsRequired(const uintptr_t* sample_include, const SampleIdInf</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataSidColIsRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sids</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;">max_sid_blen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">PedigreeIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pii</span>p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;"><span class="idiff left">SampleIdInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">siip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ParentalIdInfo</span></span><span 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">parental_id_info</span>p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maybe_modifier</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">AppendPhenoStr</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_col</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output_missing_pheno</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">omp_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_uidx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_iter</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC91" 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">@@ -3845,7 +3845,7 @@ PglErr ExportOxSampleV2(const char* outname, const uintptr_t* sample_include, co</td>
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<pre style="margin: 0;"> <span id="LC3845" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3846" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3847" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// possible todo: support column sets here</span></span>
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<pre style="margin: 0;">-<span id="LC3848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">piip</span></span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">write_parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DataParentalColsAreRequired</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sii</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="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">piip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parental_id_info</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3849" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_parents</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3850" class="line" lang="cpp"> <span class="n" style="color: #333;">writebuf_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3851" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6169,48 +6169,40 @@ PglErr ExportVcf(const uintptr_t* sample_include, const uint32_t* sample_include</td>
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6169
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6169
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<pre style="margin: 0;"> <span id="LC6169" class="line" lang="cpp"><span class="p">}</span></span>
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6170
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6170
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<pre style="margin: 0;"> <span id="LC6170" class="line" lang="cpp"></span>
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6171
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6171
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<pre style="margin: 0;"> <span id="LC6171" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">AddToFifHtable</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">htable_size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">key_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">prechar</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">htable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">key_ct_ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_idx_ptr</span><span class="p">)</span> <span class="p">{</span></span>
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6172
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<pre style="margin: 0;">-<span id="LC6172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</span><span class="p">,</span> <span class="n" style="color: #333;">htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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6173
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<pre style="margin: 0;">-<span id="LC6173" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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6174
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<pre style="margin: 0;">-<span id="LC6174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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6175
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<pre style="margin: 0;">-<span id="LC6175" 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;">key_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">key_ct_ptr</span><span class="p">;</span></span>
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6176
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<pre style="margin: 0;">-<span id="LC6176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">StoreStringAndPrecharAtEnd</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">prechar</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">key_ct</span><span class="p">])))</span> <span class="p">{</span></span>
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6177
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<pre style="margin: 0;">-<span id="LC6177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
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6178
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<pre style="margin: 0;">-<span id="LC6178" class="line" lang="cpp"> <span class="p">}</span></span>
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6179
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<pre style="margin: 0;">-<span id="LC6179" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_idx_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6180
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<pre style="margin: 0;">-<span id="LC6180" class="line" lang="cpp"> <span class="n" style="color: #333;">htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6181
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<pre style="margin: 0;">-<span id="LC6181" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">key_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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6182
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<pre style="margin: 0;">-<span id="LC6182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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6183
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<pre style="margin: 0;">-<span id="LC6183" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6184
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<pre style="margin: 0;">-<span id="LC6184" 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;">existing_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6185
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<pre style="margin: 0;">-<span id="LC6185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strequal_unsafe</span><span class="p">(</span><span class="n" style="color: #333;">existing_key</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</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="c1" style="color: #998; font-style: italic;">// Only permit this if previous instance was FILTER and this is INFO, or</span></span>
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6187
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<pre style="margin: 0;">-<span id="LC6187" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// vice versa, or this is a FORMAT key.</span></span>
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6188
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<pre style="margin: 0;">-<span id="LC6188" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// INFO entries always have prechar bit 0 set and 3 unset, while FILTER</span></span>
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6189
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<pre style="margin: 0;">-<span id="LC6189" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// entries are the reverse. FORMAT keys have prechar == 0.</span></span>
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6190
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<pre style="margin: 0;">-<span id="LC6190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">new_prechar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="n" style="color: #333;">existing_key</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">prechar</span><span class="p">;</span></span>
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6191
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<pre style="margin: 0;">-<span id="LC6191" 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;">prechar</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">new_prechar</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">9</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">9</span><span class="p">)))</span> <span class="p">{</span></span>
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6192
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6192" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Multiple "</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6193
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<pre style="margin: 0;">-<span id="LC6193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prechar</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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6194
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<pre style="margin: 0;">-<span id="LC6194" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"FILTER"</span><span class="p">);</span></span>
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6195
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<pre style="margin: 0;">-<span id="LC6195" 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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6196
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<pre style="margin: 0;">-<span id="LC6196" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"INFO"</span><span class="p">);</span></span>
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6197
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<pre style="margin: 0;">-<span id="LC6197" class="line" lang="cpp"> <span class="p">}</span></span>
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6198
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<pre style="margin: 0;">-<span id="LC6198" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">write_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="6199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6199
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<td class="diff-line-num new_line old" data-linenumber="6172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6199" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</span><span class="p">);</span></span>
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6200
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<pre style="margin: 0;">-<span id="LC6200" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">" header lines.</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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6201
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<pre style="margin: 0;">-<span id="LC6201" class="line" lang="cpp"> <span class="n" style="color: #333;">WordWrapB</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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6202
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<pre style="margin: 0;">-<span id="LC6202" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputsb</span><span class="p">();</span></span>
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6203
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<pre style="margin: 0;">-<span id="LC6203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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6204
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<pre style="margin: 0;">-<span id="LC6204" class="line" lang="cpp"> <span class="p">}</span></span>
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6205
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<pre style="margin: 0;">-<span id="LC6205" class="line" lang="cpp"> <span class="n" style="color: #333;">existing_key</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_prechar</span><span class="p">;</span></span>
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6206
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<pre style="margin: 0;">-<span id="LC6206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (3 Jan 2021): forgot to return this</span></span>
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6207
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<pre style="margin: 0;">-<span id="LC6207" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_idx_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_idx</span><span class="p">;</span></span>
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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;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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6209
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<pre style="margin: 0;">-<span id="LC6209" class="line" lang="cpp"> <span class="p">}</span></span>
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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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">htable_size</span><span class="p">)</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="n" style="color: #333;">hashval</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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6172
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<pre style="margin: 0;">+<span id="LC6172" 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;">key_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">key_ct_ptr</span><span class="p">;</span></span>
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6173
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<pre style="margin: 0;">+<span id="LC6173" class="line" lang="cpp"> <span class="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_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableAddNnt</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">TO_CONSTCPCONSTP</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">),</span> <span class="n" style="color: #333;">key_slen</span><span class="p">,</span> <span class="n" style="color: #333;">htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">key_ct</span><span class="p">,</span> <span class="n" style="color: #333;">htable</span><span class="p">);</span></span>
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6174
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<pre style="margin: 0;">+<span id="LC6174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6175
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<pre style="margin: 0;">+<span id="LC6175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">StoreStringAndPrecharAtEnd</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">prechar</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">key_ct</span><span class="p">])))</span> <span class="p">{</span></span>
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6176
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<pre style="margin: 0;">+<span id="LC6176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
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6177
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<pre style="margin: 0;">+<span id="LC6177" class="line" lang="cpp"> <span class="p">}</span></span>
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6178
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<pre style="margin: 0;">+<span id="LC6178" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_idx_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key_ct</span><span class="p">;</span></span>
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6179
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<pre style="margin: 0;">+<span id="LC6179" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">key_ct_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6180
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<pre style="margin: 0;">+<span id="LC6180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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6181
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<pre style="margin: 0;">+<span id="LC6181" class="line" lang="cpp"> <span class="p">}</span></span>
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6182
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<pre style="margin: 0;">+<span id="LC6182" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Key already present. Only permit this if previous instance was FILTER and</span></span>
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6183
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<pre style="margin: 0;">+<span id="LC6183" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this is INFO, or vice versa, or this is a FORMAT key.</span></span>
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6184
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<pre style="margin: 0;">+<span id="LC6184" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// INFO entries always have prechar bit 0 set and 3 unset, while FILTER</span></span>
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6185
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<pre style="margin: 0;">+<span id="LC6185" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// entries are the reverse. FORMAT keys have prechar == 0.</span></span>
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6186
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<pre style="margin: 0;">+<span id="LC6186" 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;">existing_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keys</span><span class="p">[</span><span class="n" style="color: #333;">cur_idx</span><span class="p">];</span></span>
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6187
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<pre style="margin: 0;">+<span id="LC6187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">new_prechar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="n" style="color: #333;">existing_key</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">prechar</span><span class="p">;</span></span>
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6188
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<pre style="margin: 0;">+<span id="LC6188" 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;">prechar</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">new_prechar</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">9</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">9</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6189
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<pre style="margin: 0;">+<span id="LC6189" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Multiple "</span><span class="p">);</span></span>
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6190
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<pre style="margin: 0;">+<span id="LC6190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prechar</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>
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6191
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<pre style="margin: 0;">+<span id="LC6191" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"FILTER"</span><span class="p">);</span></span>
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6192
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<pre style="margin: 0;">+<span id="LC6192" 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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6193
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<pre style="margin: 0;">+<span id="LC6193" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strcpya_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"INFO"</span><span class="p">);</span></span>
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6212
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6194
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<pre style="margin: 0;"> <span id="LC6194" class="line" lang="cpp"> <span class="p">}</span></span>
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6195
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<pre style="margin: 0;">+<span id="LC6195" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">write_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">':'</span><span class="p">;</span></span>
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6196
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<pre style="margin: 0;">+<span id="LC6196" class="line" lang="cpp"> <span class="n" style="color: #333;">write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">key_slen</span><span class="p">);</span></span>
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6197
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<pre style="margin: 0;">+<span id="LC6197" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">write_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">" header lines.</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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6198
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<pre style="margin: 0;">+<span id="LC6198" class="line" lang="cpp"> <span class="n" style="color: #333;">WordWrapB</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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6199
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<pre style="margin: 0;">+<span id="LC6199" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputsb</span><span class="p">();</span></span>
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6200
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<pre style="margin: 0;">+<span id="LC6200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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6213
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6201
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<pre style="margin: 0;"> <span id="LC6201" class="line" lang="cpp"> <span class="p">}</span></span>
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6202
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<pre style="margin: 0;">+<span id="LC6202" class="line" lang="cpp"> <span class="n" style="color: #333;">existing_key</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_prechar</span><span class="p">;</span></span>
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6203
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<pre style="margin: 0;">+<span id="LC6203" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (3 Jan 2021): forgot to return this</span></span>
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6204
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<pre style="margin: 0;">+<span id="LC6204" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_idx_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_idx</span><span class="p">;</span></span>
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6205
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<pre style="margin: 0;">+<span id="LC6205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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6214
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6206
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<pre style="margin: 0;"> <span id="LC6206" class="line" lang="cpp"><span class="p">}</span></span>
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6215
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6207
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<pre style="margin: 0;"> <span id="LC6207" class="line" lang="cpp"></span>
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6216
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6208
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<pre style="margin: 0;"> <span id="LC6208" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assumes ii is not in 0x80000000..0x80000007.</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">@@ -2145,8 +2145,9 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC2145" class="line" lang="cpp"><span class="s" style="color: #d14;">" (--merge-filter-mode default, not</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2146
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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="cpp"><span class="s" style="color: #d14;">" applicable to others)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2148" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"pmerge</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-list</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-info-sort</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">help_ctrl</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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2149
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<pre style="margin: 0;">-<span id="LC2149" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-info-sort <mode> : Set sort order for INFO entries when merging.</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="LC2148" class="line" lang="cpp"> <span class="n" style="color: #333;">HelpPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"pmerge</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">pmerge-list</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-pheno-sort</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">merge-info-sort</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">help_ctrl</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-pheno-sort <m> : Set sort order for phenotype columns and INFO</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="LC2150" class="line" lang="cpp"><span class="s" style="color: #d14;">" --merge-info-sort <mode> entries when merging.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2151
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<pre style="margin: 0;"> <span id="LC2151" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'none'/'0' = keep in loaded order (default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'ascii'/'a' = ASCII order</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2153
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<pre style="margin: 0;"> <span id="LC2153" class="line" lang="cpp"><span class="s" style="color: #d14;">" * 'natural'/'n' = natural sort</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14811,7 +14811,7 @@ PglErr Plink1DosageToPgen(const char* dosagename, const char* famname, const cha</td>
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<pre style="margin: 0;"> <span id="LC14811" class="line" lang=""> if (write_sid) {</span>
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<pre style="margin: 0;"> <span id="LC14812" class="line" lang=""> write_iter = strcpya_k(write_iter, "\tSID");</span>
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<pre style="margin: 0;"> <span id="LC14813" class="line" lang=""> }</span>
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<pre style="margin: 0;">-<span id="LC14814" class="line" lang=""> const uint32_t write_parents = DataParentalColsAreRequired(sample_include, &pii, sample_ct, 1);</span>
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<pre style="margin: 0;">+<span id="LC14814" class="line" lang=""> const uint32_t write_parents = DataParentalColsAreRequired(sample_include, &pii<span class="idiff left right">.sii, &pii.parental_id_info</span>, sample_ct, 1);</span>
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<pre style="margin: 0;"> <span id="LC14815" class="line" lang=""> if (write_parents) {</span>
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<pre style="margin: 0;"> <span id="LC14816" class="line" lang=""> write_iter = strcpya_k(write_iter, "\tPAT\tMAT");</span>
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<pre style="margin: 0;"> <span id="LC14817" class="line" lang=""> }</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,7 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "include/pgenlib_write.h"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_compress_stream.h"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_data.h"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_merge.h"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_psam.h"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "plink2_pvar.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -34,7 +35,8 @@ void InitPmerge(PmergeInfo* pmerge_info_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_qual_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMergeQualInfoModeNmFirst</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_filter_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMergeFilterModeNmFirst</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_info_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kMergeQualInfoModeNmFirst</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_info_sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kfSortNone</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_pheno_sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kSortNone</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_info_sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kSortNone</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_allele_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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">pmerge_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</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="63" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -63,14 +65,1157 @@ void CleanupPgenDiff(PgenDiffInfo* pgen_diff_info_ptr) {</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">free_cond</span><span class="p">(</span><span class="n" style="color: #333;">pgen_diff_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">PmergeInputFilesetStruct</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">PmergeInputFilesetLlStruct</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">PmergeInputFilesetLlStruct</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" 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;">pgen_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">psam_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">PmergeInputFileset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variant_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">grand_allele_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="p">}</span> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="n" style="color: #333;">SortFlags</span> <span class="n" style="color: #333;">sample_sort_flags</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</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="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Allocates at end of bigstack.</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"><span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">AllocFilesetLlEntry</span><span class="p">(</span><span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">filesets_endpp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC79" 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;">alloc_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RoundUpPow2</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="p">),</span> <span class="n" style="color: #333;">kEndAllocAlign</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC80" 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;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">g_bigstack_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alloc_size</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">g_bigstack_end</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">alloc_size</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">new_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">new_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">filesets_endpp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_entry</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filesets_endpp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">new_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">);</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_entry</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"><span class="p">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">LoadPmergeList</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;">list_fname</span><span class="p">,</span> <span class="n" style="color: #333;">PmergeListMode</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">main_fileset_present</span><span class="p">,</span> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">filesets_endpp</span><span class="p">)</span> <span class="p">{</span></span>
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73
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92
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<pre style="margin: 0;"> <span id="LC92" 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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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">TextStream</span> <span class="n" style="color: #333;">txs</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">PreinitTextStream</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" 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;">InitTextStream</span><span class="p">(</span><span class="n" style="color: #333;">list_fname</span><span class="p">,</span> <span class="n" style="color: #333;">kTextStreamBlenFast</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;">txs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" 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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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">pgen_suffix</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" 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;">pvar_suffix</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" 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;">psam_suffix</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPmergeListModeBfile</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">pgen_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".bed"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".bim"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">psam_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".fam"</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPmergeListModeBpfile</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">pgen_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".pgen"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".bim"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">psam_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".fam"</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">kPmergeListModePfile</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">pgen_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".pgen"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".pvar"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">psam_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="nl">default:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPmergeListModePfileVzs</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">pgen_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".pgen"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">pvar_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".pvar.zst"</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">psam_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pgen_blen</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;">pgen_suffix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" 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;">pvar_blen</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;">pvar_suffix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" 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;">psam_blen</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;">psam_suffix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" 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_single_token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglFnamesize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MAXV</span><span class="p">(</span><span class="n" style="color: #333;">pgen_blen</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" 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;">first_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TextGet</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" 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;">first_token_start</span><span class="p">)</span> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocFilesetLlEntry</span><span class="p">(</span><span class="n" style="color: #333;">filesets_endpp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" 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;">cur_entry</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" 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;">first_token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">first_token_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" 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;">first_token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_token_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" 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;">second_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">first_token_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">second_token_start</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Expand single token, using the --pmerge-list mode.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" 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;">first_token_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_single_token_slen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Entry on line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --pmerge-list file is too long.</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;">line_idx</span><span class="p">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" 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;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">first_token_slen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pgen_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pvar_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">psam_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fname_iter</span><span class="p">)))</span> <span class="p">{</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_NOMEM</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_slen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">pgen_suffix</span><span class="p">,</span> <span class="n" style="color: #333;">pgen_blen</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_slen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_suffix</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_slen</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">psam_suffix</span><span class="p">,</span> <span class="n" style="color: #333;">psam_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" 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;">second_token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">second_token_start</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" 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;">third_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">second_token_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" 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;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">third_token_start</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" 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: Line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --pmerge-list has exactly two tokens; 1 or 3 expected.</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;">line_idx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" 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;">third_token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">third_token_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" 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;">fourth_token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">third_token_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fourth_token_start</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" 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: Line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --pmerge-list has more than 3 tokens.</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;">line_idx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" 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;">second_token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">second_token_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" 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;">third_token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">third_token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">third_token_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" 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;">first_token_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kPglFnamesize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">second_token_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kPglFnamesize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">third_token_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">kPglFnamesize</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Filename on line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --pmerge-list file is too long.</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;">line_idx</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" 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;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">first_token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">second_token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">third_token_slen</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;">fname_iter</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">first_token_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">second_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">third_token_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">third_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">third_token_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">main_fileset_present</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line_idx</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="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --pmerge-list requires at least two filesets to be specified.</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="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPmergeList_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"--pmerge-list: %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" filesets specified%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;">main_fileset_present</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line_idx</span><span class="p">,</span> <span class="n" style="color: #333;">main_fileset_present</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (including main fileset)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
</pre>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="p">}</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="nl">LoadPmergeList_ret_NOMEM:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="nl">LoadPmergeList_ret_TSTREAM_FAIL:</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">TextStreamErrPrint</span><span class="p">(</span><span class="s" style="color: #d14;">"--pmerge-list file"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="nl">LoadPmergeList_ret_MALFORMED_INPUT_WW:</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">WordWrapB</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputsb</span><span class="p">();</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="nl">LoadPmergeList_ret_MALFORMED_INPUT:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="nl">LoadPmergeList_ret_INCONSISTENT_INPUT:</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetInconsistentInput</span><span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="p">}</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackReset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_mark</span><span class="p">);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="p">}</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Permanent allocations are at end of bigstack.</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">MergePsams</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">sample_sort_mode</span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filesets</span><span class="p">,</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ctp</span><span class="p">)</span> <span class="p">{</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" 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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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_end_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" 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_fname</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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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">TextStream</span> <span class="n" style="color: #333;">txs</span><span class="p">;</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">PreinitTextStream</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="p">{</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// First pass: determine sample IDs and phenotype set.</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Intermission: sort sample and phenotype IDs.</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Second pass: populate data structure, then call WritePsam().</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Allocate a single linebuf that's used in all first-pass loads, so that</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we can have the pheno strset grow from bigstack_end down in an</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// unfragmented manner.</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">linebuf_capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MINV</span><span class="p">(</span><span class="n" style="color: #333;">kMaxLongLine</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_left</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kDecompressChunkSize</span><span class="p">;</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" 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;">linebuf</span><span class="p">;</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">linebuf_capacity</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">linebuf</span><span class="p">)))</span> <span class="p">{</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="p">}</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If --sample-inner-join is specified, we append raw null-terminated</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sample-ID strings to the bottom of bigstack while scanning the first</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// file, construct the usual non-resizable string-hash-table data structure</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// when we're done. Each ID then has a 0-based index, and we use</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sample_include/cur_sample_include to track which sample IDs are present</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in all files from that point on.</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Otherwise, we add sample IDs to the resizable sample_id_strset data</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// structure and wait till we've processed all files before ordering the</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// elements.</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Analogous thing happens for phenotype names if --pheno-inner-join is</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// specified. Phenotype-name data structure grows down from the top of</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bigstack.</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeFlags</span> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pmip</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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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">first_sample_ids_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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263
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<pre style="margin: 0;">+<span id="LC263" 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;">first_sample_ids</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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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">first_sample_ids_htable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" 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;">cur_sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" 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;">sample_id_strset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">first_sample_id_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_id_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">kfPmergeSampleInnerJoin</span><span class="p">)</span> <span class="p">{</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">);</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// - arena_bottom tracks the current append point</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// - first_sample_ids, first_sample_ids_htable, sample_include,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cur_sample_include allocated after we're done scanning first file</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// - sample_id_table_size set to first_sample_ids_htable size at that</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// point</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_calloc_cp</span><span class="p">(</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_id_strset</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="p">}</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="p">}</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="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;">first_pheno_names</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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283
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<pre style="margin: 0;">+<span id="LC283" 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;">first_pheno_names_htable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" 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;">pheno_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 new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" 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;">cur_pheno_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 new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">pheno_strset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">first_pheno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_names_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfPmergePhenoInnerJoin</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_calloc_cp</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">)))</span> <span class="p">{</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="p">}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="p">}</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arena_bottom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" 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;">arena_top</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" 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;">decompress_thread_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAXV</span><span class="p">(</span><span class="n" style="color: #333;">max_thread_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" 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;">idbuf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_textbuf</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_sample_id_blen_m2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets_iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" 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;">TextStreamOpenEx</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxLongLine</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf_capacity</span><span class="p">,</span> <span class="n" style="color: #333;">decompress_thread_ct</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">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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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="p">}</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Worth optimizing this more than most text-reading loops, since we may</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// be processing a LOT of files.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" 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;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TextLineEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" 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;">TextGetUnsafe2K</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line_start</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: No samples in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tokequal_k</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="s" style="color: #d14;">"FID"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tokequal_k</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="s" style="color: #d14;">"IID"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">line_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_blen</span><span class="p">;</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span><span class="p">;</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">postid_pat_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">postid_mat_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">fid_present</span><span class="p">;</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="p">{</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" 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;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">);</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" 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;">iid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">);</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstPrechar</span><span class="p">(</span><span class="n" style="color: #333;">iid_start</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strequal_k</span><span class="p">(</span><span class="n" style="color: #333;">iid_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"IID"</span><span class="p">,</span> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iid_start</span><span class="p">)))</span> <span class="p">{</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="p">}</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="p">}</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">);</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"SID"</span><span class="p">))</span> <span class="p">{</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">sid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]));</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">token_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
355
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<pre style="margin: 0;">+<span id="LC355" 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;">postid_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">token_start</span><span class="p">);</span> <span class="n" style="color: #333;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">token_end</span><span class="p">),</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">postid_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">);</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="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;">token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">token_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">token_slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
359
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<pre style="margin: 0;">+<span id="LC359" 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;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"FID"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)))</span> <span class="p">{</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
361
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<pre style="margin: 0;">+<span id="LC361" 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: Duplicate FID column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
363
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<pre style="margin: 0;">+<span id="LC363" 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: Improperly positioned FID column in %s (must be first).</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_fname</span><span class="p">);</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
367
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<pre style="margin: 0;">+<span id="LC367" 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;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"IID"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
368
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<pre style="margin: 0;">+<span id="LC368" 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: Duplicate IID column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="p">}</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" 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;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"SID"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sid_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="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: Duplicate SID column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC375" 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: Improperly positioned SID column in %s (must immediately follow IID).</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_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"PAT"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="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;">postid_pat_col_idx</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="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: Duplicate PAT column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">postid_pat_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">postid_col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"MAT"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">postid_mat_col_idx</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="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: Duplicate MAT column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">postid_mat_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">postid_col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"SEX"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="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;">token_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxIdBlen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Phenotype names are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">token_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">max_pheno_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="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;">StrsetAddEndResize</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="n" style="color: #333;">token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxPhenoCt</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMaxPhenoCt</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" does not support more than "</span> <span class="n" style="color: #333;">MAX_PHENO_CT_STR</span> <span class="s" style="color: #d14;">" phenotypes.</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 new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max_pheno_name_blen calculation deferred since any name may not</span></span>
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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// appear in a later file</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">)</span> <span class="p">{</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// StoreStringAtEnd(), without dst assignment</span></span>
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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
418
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<pre style="margin: 0;">+<span id="LC418" 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;">PtrWSubCk</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">token_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="n" style="color: #333;">arena_top</span><span class="p">)))</span> <span class="p">{</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="n" style="color: #333;">token_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">first_pheno_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
423
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<pre style="margin: 0;">+<span id="LC423" 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;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
424
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<pre style="margin: 0;">+<span id="LC424" 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;">pheno_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableFindNnt</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">,</span> <span class="n" style="color: #333;">token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">);</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">cur_pheno_include</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_idx</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
427
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<pre style="margin: 0;">+<span id="LC427" 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: Duplicate phenotype name '%s' in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">],</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_include</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="p">}</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">postid_mat_col_idx</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
436
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<pre style="margin: 0;">+<span id="LC436" 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: %s has a '%cAT' column without a '%cAT' column; either both or neither must be present.</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_fname</span><span class="p">,</span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'P'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">,</span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">);</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="p">}</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" 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;">line_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" 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;">line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">line_blen</span><span class="p">)</span> <span class="p">{</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_blen</span><span class="p">;</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="p">}</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">TextGetUnsafe2K</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line_start</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: No samples in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// .fam</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfFamCol1</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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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfFamCol34</span><span class="p">)</span> <span class="p">{</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">postid_pat_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">postid_mat_col_idx</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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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfFamCol6</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">StrsetAddEndResize</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="s" style="color: #d14;">"PHENO1"</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">),</span> <span class="n" style="color: #333;">kMaxPhenoCt</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kMaxPhenoCt</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" does not support more than "</span> <span class="n" style="color: #333;">MAX_PHENO_CT_STR</span> <span class="s" style="color: #d14;">" phenotypes.</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="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="p">}</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">max_pheno_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="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;">first_pheno_names_htable</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
474
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<pre style="margin: 0;">+<span id="LC474" 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;">PtrWSubCk</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">)))</span> <span class="p">{</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="p">}</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top</span><span class="p">),</span> <span class="s" style="color: #d14;">"PHENO1"</span><span class="p">);</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">first_pheno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
479
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<pre style="margin: 0;">+<span id="LC479" 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;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="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;">pheno_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableFind</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">,</span> <span class="n" style="color: #333;">TO_CONSTCPCONSTP</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_names</span><span class="p">),</span> <span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">),</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">);</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_include</span><span class="p">);</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="p">}</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="p">}</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="p">}</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="p">}</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">first_parent_postid_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">parent_col_skip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">postid_mat_col_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">first_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">second_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">postid_mat_col_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">first_parent_postid_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">postid_mat_col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">parent_col_skip</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">parent_col_skip</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">first_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">second_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="p">}</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="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;">fid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">g_one_char_strs</span><span class="p">[</span><span class="mi" style="color: #099;">96</span><span class="p">]);</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">fid_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" 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;">sid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">g_one_char_strs</span><span class="p">[</span><span class="mi" style="color: #099;">96</span><span class="p">]);</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sid_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" 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;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" 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;">fid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">fid_start</span><span class="p">);</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">fid_start</span><span class="p">;</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">fid_end</span><span class="p">);</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="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;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">token_start</span><span class="p">)))</span> <span class="p">{</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MISSING_TOKENS</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="p">}</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" 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;">iid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_start</span><span class="p">;</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">iid_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" 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;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iid_end</span><span class="p">;</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">iid_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iid_start</span><span class="p">;</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sid_present</span><span class="p">)</span> <span class="p">{</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">sid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">);</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">);</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">sid_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sid_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">sid_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="p">(</span><span class="n" style="color: #333;">sid_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sid_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
523
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<pre style="margin: 0;">+<span id="LC523" 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;">sid_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxIdBlen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: SIDs are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="p">}</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">iid_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_sample_id_blen_m2</span><span class="p">)</span> <span class="p">{</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sample_id_blen_m2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">iid_slen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
533
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<pre style="margin: 0;">+<span id="LC533" 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;">max_sample_id_blen_m2</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;">kMaxIdSlen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: FIDs and IIDs are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="p">}</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="p">}</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" 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;">id_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">fid_start</span><span class="p">,</span> <span class="n" style="color: #333;">fid_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">id_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">id_iter</span><span class="p">,</span> <span class="n" style="color: #333;">iid_start</span><span class="p">,</span> <span class="n" style="color: #333;">iid_slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="n" style="color: #333;">id_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">id_iter</span><span class="p">,</span> <span class="n" style="color: #333;">sid_start</span><span class="p">,</span> <span class="n" style="color: #333;">sid_slen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"> <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="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
542
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<pre style="margin: 0;">+<span id="LC542" 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;">id_slen</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;">idbuf</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_id_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
544
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<pre style="margin: 0;">+<span id="LC544" 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;">StrsetAddResize</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">id_slen</span><span class="p">,</span> <span class="mi" style="color: #099;">2U</span> <span class="o" style="font-weight: 600;">*</span> <span class="mh" style="color: #099;">0x7ffffffe</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_strset</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x7ffffffe</span><span class="p">)</span> <span class="p">{</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" does not support more than 2^31 - 2 samples.</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="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
552
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<pre style="margin: 0;">+<span id="LC552" 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;">first_sample_ids_htable</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
553
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<pre style="margin: 0;">+<span id="LC553" 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;">id_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">)))</span> <span class="p">{</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="p">}</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_bottom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyua</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">id_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
557
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<pre style="margin: 0;">+<span id="LC557" 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;">first_sample_id_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x7ffffffe</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" does not support more than 2^31 - 2 samples.</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="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableFind</span><span class="p">(</span><span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids_htable</span><span class="p">,</span> <span class="n" style="color: #333;">id_slen</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_table_size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">IsSet</span><span class="p">(</span><span class="n" style="color: #333;">cur_sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">sample_idx</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">TabsToSpaces</span><span class="p">(</span><span class="n" style="color: #333;">idbuf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
567
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<pre style="margin: 0;">+<span id="LC567" 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: Duplicate sample ID </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="p">}</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_sample_include</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="p">}</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_parent_postid_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">first_parent_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NextTokenMult</span><span class="p">(</span><span class="n" style="color: #333;">token_end</span><span class="p">,</span> <span class="n" style="color: #333;">first_parent_postid_col_idx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">first_parent_start</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MISSING_TOKENS</span><span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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;">first_parent_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">first_parent_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
580
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<pre style="margin: 0;">+<span id="LC580" 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;">first_parent_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_parent_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_parent_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_parent_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">first_parent_max_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
582
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<pre style="margin: 0;">+<span id="LC582" 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;">first_parent_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxIdSlen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
583
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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="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: FIDs and IIDs are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="n" style="color: #333;">first_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_parent_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
588
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<pre style="margin: 0;">+<span id="LC588" 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;">second_parent_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NextTokenMult</span><span class="p">(</span><span class="n" style="color: #333;">first_parent_end</span><span class="p">,</span> <span class="n" style="color: #333;">parent_col_skip</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
589
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<pre style="margin: 0;">+<span id="LC589" 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;">second_parent_start</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MISSING_TOKENS</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">second_parent_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
593
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<pre style="margin: 0;">+<span id="LC593" 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;">second_parent_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">second_parent_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">second_parent_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">second_parent_max_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
595
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<pre style="margin: 0;">+<span id="LC595" 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;">second_parent_slen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kMaxIdSlen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: FIDs and IIDs are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">second_parent_max_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_parent_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
602
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<pre style="margin: 0;">+<span id="LC602" 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;">line_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">token_end</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
603
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<pre style="margin: 0;">+<span id="LC603" 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;">line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">line_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">line_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">max_line_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_blen</span><span class="p">;</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
609
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<pre style="margin: 0;">+<span id="LC609" 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;">TextGetUnsafe2K</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line_start</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
612
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<pre style="margin: 0;">+<span id="LC612" 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;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
613
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<pre style="margin: 0;">+<span id="LC613" 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: Line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of %s starts with a '#'. (This is only permitted before the first nonheader line, and if a #FID/IID header line is present it must denote the end of the header block.)</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;">line_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
620
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<pre style="margin: 0;">+<span id="LC620" 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;">CleanupTextStream2</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">postid_mat_col_idx</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">postid_pat_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_parent_max_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_parent_max_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
627
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<pre style="margin: 0;">+<span id="LC627" 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 new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">second_parent_max_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_parent_max_blen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_sample_ids_start</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
633
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<pre style="margin: 0;">+<span id="LC633" 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;">first_sample_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">filesets</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">ArenaBaseSet</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_id_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetHtableFastSize</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
637
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<pre style="margin: 0;">+<span id="LC637" 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;">arena_bottom</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">arena_top</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_alloc_kcp</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_sample_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
</pre>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_sample_ids_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_include</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_sample_include</span><span class="p">)))</span> <span class="p">{</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="p">}</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllBits</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">);</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" 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;">first_sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_sample_ids_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_sample_ids_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_ids_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
650
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<pre style="margin: 0;">+<span id="LC650" 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;">IdHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_ids_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
651
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<pre style="margin: 0;">+<span id="LC651" 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;">mutable_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">K_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ids_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">TabsToSpaces</span><span class="p">(</span><span class="n" style="color: #333;">mutable_id</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
653
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<pre style="margin: 0;">+<span id="LC653" 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: Duplicate sample ID </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">mutable_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="p">}</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_ids_iter</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="p">}</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" 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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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAnd</span><span class="p">(</span><span class="n" style="color: #333;">cur_sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">);</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" 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;">AllWordsAreZero</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ctl</span><span class="p">)))</span> <span class="p">{</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" 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: No common samples in --pmerge%s --sample-inner-join job.</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;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"-list"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_2</span><span class="p">;</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="p">}</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="p">}</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">cur_sample_include</span><span class="p">);</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="p">}</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" 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;">pheno_strset</span><span class="p">)</span> <span class="p">{</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" 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;">first_pheno_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_ct</span><span class="p">);</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">filesets</span><span class="p">)</span> <span class="p">{</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// must handle pheno_ct == 0</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// (only really need to set first_pheno_names_htable to non-null in</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that case, since that's how we currently recognize we aren't</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// processing the first .psam file)</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" 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;">pheno_names_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top</span><span class="p">);</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">ArenaEndSet</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">);</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetHtableFastSize</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_ct</span><span class="p">);</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" 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;">arena_end_alloc_kcp</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_pheno_names</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_end_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_end_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_include</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_end_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">arena_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_pheno_include</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="p">}</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllBits</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_include</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_pheno_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
687
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<pre style="margin: 0;">+<span id="LC687" 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;">pheno_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;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">first_pheno_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">first_pheno_names</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_names_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
690
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<pre style="margin: 0;">+<span id="LC690" 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;">IdHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_iter</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_idx</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
691
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<pre style="margin: 0;">+<span id="LC691" 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: Duplicate phenotype name '%s' in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_iter</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_iter</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
696
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<pre style="margin: 0;">+<span id="LC696" 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;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">BitvecAnd</span><span class="p">(</span><span class="n" style="color: #333;">cur_pheno_include</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">);</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">pheno_include</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">);</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">first_pheno_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_include</span><span class="p">);</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="p">}</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="p">}</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets_iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">filesets_iter</span><span class="p">);</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Intermission:</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. Move final set of phenotype ID strings to bottom, compute</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max_pheno_name_blen if --pheno-inner-join.</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2. Compute max_sample_id_blen and max_sid_blen if --sample-inner-join.</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 3. Free all end-of-bigstack allocations.</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 4. Construct SampleIdInfo at end of bigstack, to be returned.</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5. Construct pheno_names, hash tables.</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names</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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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names_htable</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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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_id_htable</span><span class="p">;</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_ctl</span><span class="p">;</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="p">{</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="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_tmp_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">arena_bottom</span><span class="p">);</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names_tmp_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" 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;">byte_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_strset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">arena_top</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">memmove</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_tmp_start</span><span class="p">,</span> <span class="n" style="color: #333;">arena_top</span><span class="p">,</span> <span class="n" style="color: #333;">byte_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_tmp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_tmp_start</span><span class="p">[</span><span class="n" style="color: #333;">byte_ct</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">max_pheno_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_names_tmp_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">first_pheno_names</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;">pheno_names_write_iter</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">kMaxIdBlen</span><span class="p">)</span> <span class="p">{</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ensure memcpy is safe</span></span>
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<td class="diff-line-num new new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">pheno_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 new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" 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;">pheno_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;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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<pre style="margin: 0;">+<span id="LC734" 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;">pheno_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">pheno_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_uidx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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<pre style="margin: 0;">+<span id="LC735" 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_pheno_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_pheno_names</span><span class="p">[</span><span class="n" style="color: #333;">pheno_uidx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
736
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<pre style="margin: 0;">+<span id="LC736" 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;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">cur_pheno_name</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="n" style="color: #333;">max_pheno_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_name</span><span class="p">,</span> <span class="n" style="color: #333;">blen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="p">}</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_tmp_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_names_write_iter</span><span class="p">;</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackBaseSet</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_tmp_end</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_id_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_sample_id_blen_m2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC750" 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;">first_sample_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">first_sample_id_ct</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">first_sample_ctl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">sample_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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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_include</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_uidx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC758" 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_sample_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">sample_uidx</span><span class="p">];</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" 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;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToDelim</span><span class="p">(</span><span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">cur_sample_id</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">),</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_id_blen_m1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cur_sample_id</span><span class="p">;</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">sample_id_blen_m1</span><span class="p">)</span> <span class="p">{</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_id_blen_m1</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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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"> <span class="p">}</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" 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;">sid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" 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;">sid_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;">sid_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">sid_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="p">(</span><span class="n" style="color: #333;">sid_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">))</span> <span class="p">{</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">sid_slen</span><span class="p">)</span> <span class="p">{</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sid_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"> <span class="p">}</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="p">}</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"> <span class="p">}</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// defensive</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"> <span class="n" style="color: #333;">linebuf</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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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="n" style="color: #333;">first_pheno_names</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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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"> <span class="n" style="color: #333;">first_pheno_names_htable</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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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_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 new new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_pheno_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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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_strset</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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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="cpp"></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">);</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kfSampleIdFidPresent</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">kfSampleIdParentsPresent</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMiscStrictSid0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// affects --indiv-sort</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfSampleIdStrictSid0</span><span class="p">;</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"> <span class="p">}</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">;</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">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;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">))))</span> <span class="p">{</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="p">}</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// place this below optional siip->sids, so that</span></span>
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<td class="diff-line-num new new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// BigstackEndSet(siip->sample_ids) is always correct on success</span></span>
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<td class="diff-line-num new new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">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;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="cpp"> <span class="p">}</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetHtableFastSize</span><span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">max_pheno_name_blen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_names</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_end_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_names_htable</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"> <span class="p">}</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="cpp"> <span class="p">}</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
808
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<pre style="margin: 0;">+<span id="LC808" 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;">sample_ids_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_id_strset</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ids_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_id_strset</span><span class="p">[</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
812
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<pre style="margin: 0;">+<span id="LC812" 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;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToDelim</span><span class="p">(</span><span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_read_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">),</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ids_read_iter</span><span class="p">,</span> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sample_ids_read_iter</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_ids_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_write_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
815
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<pre style="margin: 0;">+<span id="LC815" 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;">sid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strnul</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
817
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<pre style="margin: 0;">+<span id="LC817" 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;">sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">iid_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
818
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<pre style="margin: 0;">+<span id="LC818" 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;">sid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
819
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<pre style="margin: 0;">+<span id="LC819" 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="p">(</span><span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">]),</span> <span class="n" style="color: #333;">sid_start</span><span class="p">,</span> <span class="n" style="color: #333;">sid_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_ids_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sid_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">sample_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 new new_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">cur_bits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_include</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitIter1</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_uidx_base</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur_bits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
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<pre style="margin: 0;">+<span id="LC828" 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_sample_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">sample_uidx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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<pre style="margin: 0;">+<span id="LC829" 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;">iid_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvToDelim</span><span class="p">(</span><span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">cur_sample_id</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">),</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpyx</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">cur_sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">iid_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cur_sample_id</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_ids_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_write_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
833
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<pre style="margin: 0;">+<span id="LC833" 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;">sid_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">iid_end</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">[</span><span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">]),</span> <span class="n" style="color: #333;">sid_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="p">}</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// defensive</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids_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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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids</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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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">first_sample_ids_htable</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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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_sample_include</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_id_strset</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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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">g_bigstack_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bigstack_mark</span><span class="p">;</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" 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;">pheno_names_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_names_tmp_start</span><span class="p">;</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// phenotypes are stored in reverse</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_names_write_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names</span><span class="p">[</span><span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
852
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<pre style="margin: 0;">+<span id="LC852" 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;">pheno_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span> <span class="n" style="color: #333;">pheno_idx</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">;</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_write_iter</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">;</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">);</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_write_iter</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">[</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"> <span class="p">}</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">pheno_sort_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_pheno_sort</span><span class="p">;</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_sort_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kSortAscii</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strcmp_overread_casted</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<pre style="margin: 0;">+<span id="LC862" 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;">pheno_sort_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kSortNatural</span><span class="p">)</span> <span class="p">{</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strcmp_natural</span><span class="p">);</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"> <span class="p">}</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
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<pre style="margin: 0;">+<span id="LC868" 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;">pheno_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;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"> <span class="n" style="color: #333;">HtableAddNondup</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_idx</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_names_read_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_names_read_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">]);</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> <span class="p">}</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="p">}</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_include</span><span class="p">)))</span> <span class="p">{</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="p">}</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllBits</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">);</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" 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;">sample_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" 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;">sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">;</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_sort_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kSortNone</span><span class="p">)</span> <span class="p">{</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_sort_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kSortFile</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// yes, this is a bit circuitous</span></span>
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<td class="diff-line-num new new_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_end_mark2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" 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;">new_sample_idx_to_old</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
886
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<pre style="margin: 0;">+<span id="LC886" 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;">sample_ids_tmp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_ids_tmp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
891
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<pre style="margin: 0;">+<span id="LC891" 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;">sids_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sids_tmp</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
897
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<pre style="margin: 0;">+<span id="LC897" 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;">SampleSortFileMap</span><span class="p">(</span><span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_1</span><span class="p">;</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
901
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<pre style="margin: 0;">+<span id="LC901" 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;">new_sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ids_tmp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
902
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<pre style="margin: 0;">+<span id="LC902" 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;">new_sids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sids_tmp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">new_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">new_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">new_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">old_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_sample_idx_to_old</span><span class="p">[</span><span class="n" style="color: #333;">new_idx</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_ids_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">[</span><span class="n" style="color: #333;">old_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp"> <span class="n" style="color: #333;">new_sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">new_sample_ids_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">]);</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sids</span><span class="p">)</span> <span class="p">{</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">new_sids_iter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sids</span><span class="p">[</span><span class="n" style="color: #333;">old_idx</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">]));</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp"> <span class="n" style="color: #333;">new_sids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">new_sids_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">]);</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="p">}</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ids_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sids</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">sids</span><span class="p">,</span> <span class="n" style="color: #333;">sids_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_sid_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackEndReset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_mark2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_sort_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kSortAscii</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strcmp_overread_casted</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// natural-sort, even if sample_sort_mode == kSort0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"> <span class="n" style="color: #333;">qsort</span><span class="p">(</span><span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strcmp_natural</span><span class="p">);</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="p">}</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"> <span class="p">}</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_id_table_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetHtableFastSize</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_id_htable</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_htable</span><span class="p">);</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sample_ids_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<pre style="margin: 0;">+<span id="LC935" 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_sample_id</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
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<pre style="margin: 0;">+<span id="LC936" 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;">sids_iter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_sample_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ids_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
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<pre style="margin: 0;">+<span id="LC939" 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;">id_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpyax</span><span class="p">(</span><span class="n" style="color: #333;">idbuf</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ids_iter</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" 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;">sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">sids_iter</span><span class="p">);</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">id_iter</span><span class="p">,</span> <span class="n" style="color: #333;">sids_iter</span><span class="p">,</span> <span class="n" style="color: #333;">sid_blen</span><span class="p">);</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sid_blen</span><span class="p">;</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="n" style="color: #333;">sids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">sids_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">]);</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_sample_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idbuf</span><span class="p">;</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="p">}</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">HtableAddNondup</span><span class="p">(</span><span class="n" style="color: #333;">cur_sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_table_size</span><span class="p">,</span> <span class="n" style="color: #333;">sample_idx</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id_htable</span><span class="p">);</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="cpp"> <span class="p">}</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="p">}</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="n" style="color: #333;">linebuf_capacity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAXV</span><span class="p">(</span><span class="n" style="color: #333;">max_line_blen</span><span class="p">,</span> <span class="n" style="color: #333;">kDecompressMinBlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kDecompressChunkSize</span><span class="p">;</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// max_{p,m}aternal_id_blen may be overestimated in --sample-inner-join</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// case, but that's harmless since we free this strbox soon enough</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">ParentalIdInfo</span> <span class="n" style="color: #333;">parental_id_info</span><span class="p">;</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">;</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male</span><span class="p">;</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">paternal_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">maternal_ids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_nm</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sex_male</span><span class="p">)))</span> <span class="p">{</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"> <span class="p">}</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="p">{</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" 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;">paternal_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">paternal_ids</span><span class="p">;</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" 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;">maternal_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">maternal_ids</span><span class="p">;</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">sample_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sample_idx</span><span class="p">)</span> <span class="p">{</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">paternal_ids_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">paternal_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">paternal_ids_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">]);</span></span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy_k</span><span class="p">(</span><span class="n" style="color: #333;">maternal_ids_iter</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">maternal_ids_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">maternal_ids_iter</span><span class="p">[</span><span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">]);</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="p">}</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="p">}</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">max_paternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_paternal_id_blen</span><span class="p">;</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">parental_id_info</span><span class="p">.</span><span class="n" style="color: #333;">max_maternal_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_maternal_id_blen</span><span class="p">;</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="cpp"></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// unlike core pheno_cols, this just lives on bigstack</span></span>
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<td class="diff-line-num new new_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">BIGSTACK_ALLOC_X</span><span class="p">(</span><span class="n" style="color: #333;">PhenoCol</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_cols</span><span class="p">)))</span> <span class="p">{</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="p">}</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" 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;">pheno_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;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">)</span> <span class="p">{</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we don't really distinguish between case/control and quantitative</span></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// phenotypes here (just use data.qt in both cases), and it should be</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ok to overallocate a bit in the categorical-phenotype case</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">sample_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">].</span><span class="n" style="color: #333;">nonmiss</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_d</span><span class="p">(</span><span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">qt</span><span class="p">))))</span> <span class="p">{</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="p">}</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We use kPhenoDtypeCc instead of kPhenoTypeOther to indicate "type</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// not yet known", since that lets us leave it unchanged if all values</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// are missing.</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">].</span><span class="n" style="color: #333;">type_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPhenoDtypeCc</span><span class="p">;</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// defensive</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">].</span><span class="n" style="color: #333;">category_names</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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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">].</span><span class="n" style="color: #333;">nonnull_category_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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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="cpp"> <span class="p">}</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="p">}</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" 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_mark2</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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999
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<pre style="margin: 0;">+<span id="LC999" 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;">kNonphenoColCt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" 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_col_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kNonphenoColCt</span><span class="p">;</span></span>
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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;">// note that ZeroWArr(pheno_ctl, pheno_include) is safe when pheno_ct == 0</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" 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;">pheno_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">);</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" 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;">col_skips</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1004
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<pre style="margin: 0;">+<span id="LC1004" 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;">col_types</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1005
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<pre style="margin: 0;">+<span id="LC1005" 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;">token_ptrs</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1006
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<pre style="margin: 0;">+<span id="LC1006" 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;">token_slens</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">max_col_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">col_skips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">max_col_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">col_types</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_kcp</span><span class="p">(</span><span class="n" style="color: #333;">max_col_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_ptrs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_u32</span><span class="p">(</span><span class="n" style="color: #333;">max_col_ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">token_slens</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_w</span><span class="p">(</span><span class="n" style="color: #333;">pheno_ctl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_include</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">linebuf_capacity</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">linebuf</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// phenotype-major</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" 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;">pheno_locked</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">merge_pheno_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kMergePhenoModeNmFirst</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// no need to check for overflow in 32-bit case since we would have</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// already run out of memory on data.qt allocations</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">bit_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_calloc_w</span><span class="p">(</span><span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">bit_ct</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pheno_locked</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_NOMEM</span><span class="p">;</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="p">}</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"> <span class="p">}</span></span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"--pmerge%s: %u sample%s and %u phenotype%s present.</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;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"-list"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"s"</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"s"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintf</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;">"--pmerge%s: %u sample%s present.</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;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"-list"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">sample_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"s"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [category_names] [category_names_htable] [strings]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ^ ^ ^ ^</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// | | | |</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// g_bigstack_base arena_bottom arena_top g_bigstack_end</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// category-name strings are allocated at the end of bigstack, and need to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// remain allocated until WritePsam() returns.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// category_names_htable is repositioned, resized, and rebuilt whenever</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// category_names would otherwise overflow.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// No other allocations allowed past this point, until WritePsam() call.</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_bottom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">arena_top</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" 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;">category_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// uint32_t* category_names_htable = nullptr;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">category_names_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// category_names_capacity == category_names_htable_size / 2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// uint32_t category_names_htable_size = 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// possible todo: track seen realpaths, skip duplicates</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets_iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1052
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<pre style="margin: 0;">+<span id="LC1052" 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;">TextStreamOpenEx</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxLongLine</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf_capacity</span><span class="p">,</span> <span class="n" style="color: #333;">decompress_thread_ct</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">linebuf</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_REWIND_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
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<pre style="margin: 0;">+<span id="LC1056" 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;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TextLineEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
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<pre style="margin: 0;">+<span id="LC1058" 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;">TextGetUnsafe2K</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line_start</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="74" style="width: 35px; color: rgba(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="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" 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;">TextStreamRawErrcode</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_REWIND_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tokequal_k</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="s" style="color: #d14;">"FID"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tokequal_k</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="s" style="color: #d14;">"IID"</span><span class="p">))</span> <span class="p">{</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="p">}</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="n" style="color: #333;">ZeroWArr</span><span class="p">(</span><span class="n" style="color: #333;">pheno_ctl</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// uint32_t sid_present = 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// uint32_t parents_present = 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// uint32_t sex_present = 0;</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">fid_present</span><span class="p">;</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">;</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</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;">0</span><span class="p">;</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"> <span class="n" style="color: #333;">relevant_postfid_col_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">fid_present</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" 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;">fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</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;">0</span><span class="p">;</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" 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;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">line_start</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" 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;">col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" 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;">token_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FirstNonTspace</span><span class="p">(</span><span class="n" style="color: #333;">token_end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IsEolnKns</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">token_start</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="cpp"> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurTokenEnd</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" 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;">token_slen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">token_start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">token_slen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"IID"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"SID"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sid_present = 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"PAT"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parents_present = 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"MAT"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal_k</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="s" style="color: #d14;">"SEX"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sex_present = 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">token_slen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StrboxHtableFind</span><span class="p">(</span><span class="n" style="color: #333;">token_start</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_htable</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">);</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> <span class="p">}</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">cur_col_type</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_col_type</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">kNonphenoColCt</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_col_type</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" 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;">rpf_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">relevant_postfid_col_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">rpf_col_idx</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">rpf_col_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">rpf_col_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">rpf_col_idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="cpp"> <span class="n" style="color: #333;">line_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdvPastDelim</span><span class="p">(</span><span class="n" style="color: #333;">token_end</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">line_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" 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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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// .fam</span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"> <span class="n" style="color: #333;">fid_present</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">kfFamCol1</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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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</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;">fid_present</span><span class="p">;</span></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"> <span class="n" style="color: #333;">relevant_postfid_col_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfFamCol34</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parents_present = 1;</span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="p">}</span></span>
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1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfFamCol5</span><span class="p">)</span> <span class="p">{</span></span>
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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sex_present = 1;</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="p">}</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fam_cols</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfFamCol6</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"> <span class="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;">pheno_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StrboxHtableFind</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names_htable</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"PHENO1"</span><span class="p">),</span> <span class="n" style="color: #333;">pheno_names_table_size</span><span class="p">);</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="n" style="color: #333;">relevant_postfid_col_ct</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;">kNonphenoColCt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pheno_idx</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_include</span><span class="p">);</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">TextStreamErrcode2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_TSTREAM_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1151
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<pre style="margin: 0;">+<span id="LC1151" 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;">CleanupTextStream2</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="cpp"> <span class="n" style="color: #333;">filesets_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesets_iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">filesets_iter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackReset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_mark2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackEndSet</span><span class="p">(</span><span class="n" style="color: #333;">arena_top</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">category_names_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cpp"> <span class="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;">category_names_final</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">R_CAST</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackBaseSet</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">category_names_final</span><span class="p">[</span><span class="n" style="color: #333;">category_names_ct</span><span class="p">]));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="n" style="color: #333;">memmove</span><span class="p">(</span><span class="n" style="color: #333;">category_names_final</span><span class="p">,</span> <span class="n" style="color: #333;">category_names</span><span class="p">,</span> <span class="n" style="color: #333;">category_names_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">intptr_t</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"> <span class="n" style="color: #333;">category_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">category_names_final</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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1165
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<pre style="margin: 0;">+<span id="LC1165" 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;">pheno_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;">pheno_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">)</span> <span class="p">{</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="cpp"> <span class="n" style="color: #333;">PhenoCol</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pheno_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">pheno_cols</span><span class="p">[</span><span class="n" style="color: #333;">pheno_idx</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pheno_col</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">type_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPhenoDtypeQt</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kfMiscAffection01</span><span class="p">)</span> <span class="p">{</span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO</span></span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If all values are in {0, 1, missing}, convert to {1, 2, missing}</span></span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1172
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<pre style="margin: 0;">+<span id="LC1172" 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;">pheno_col</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">type_code</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPhenoDtypeCat</span><span class="p">)</span> <span class="p">{</span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="cpp"> <span class="n" style="color: #333;">pheno_col</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">category_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">category_names</span><span class="p">;</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="cpp"> <span class="p">}</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"> <span class="p">}</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="cpp"> <span class="p">;;;</span></span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">kMaxOutfnameExtBlen</span><span class="p">,</span> <span class="s" style="color: #d14;">".psam"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" 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;">WritePsam</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">sample_include</span><span class="p">,</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">parental_id_info</span><span class="p">,</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_cols</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_names</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="s" style="color: #d14;">"NA"</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_pheno_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">kfPsamColDefault</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">MergePsams_ret_1</span><span class="p">;</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="cpp"> <span class="p">}</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"--pmerge%s: Merged .psam written to %s .</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"-list"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">);</span></span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sample_ctp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_ct</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="cpp"> <span class="n" style="color: #333;">ArenaEndSet</span><span class="p">(</span><span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sample_ids</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bigstack_end_mark</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="cpp"> <span class="nl">MergePsams_ret_NOMEM:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="cpp"> <span class="nl">MergePsams_ret_TSTREAM_REWIND_FAIL:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="cpp"> <span class="n" style="color: #333;">TextStreamErrPrintRewind</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="cpp"> <span class="nl">MergePsams_ret_TSTREAM_FAIL:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="cpp"> <span class="n" style="color: #333;">TextStreamErrPrint</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">);</span></span>
</pre>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="cpp"> <span class="nl">MergePsams_ret_MISSING_TOKENS:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1198
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<pre style="margin: 0;">+<span id="LC1198" 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: Line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of %s has fewer tokens than expected.</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;">line_idx</span><span class="p">,</span> <span class="n" style="color: #333;">cur_fname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="cpp"> <span class="nl">MergePsams_ret_MALFORMED_INPUT_WW:</span></span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="cpp"> <span class="n" style="color: #333;">WordWrapB</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="cpp"> <span class="nl">MergePsams_ret_MALFORMED_INPUT_2:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputsb</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="cpp"> <span class="nl">MergePsams_ret_MALFORMED_INPUT:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetMalformedInput</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(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="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="cpp"> <span class="nl">MergePsams_ret_INCONSISTENT_INPUT:</span></span>
</pre>
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1207
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<pre style="margin: 0;">+<span id="LC1207" 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;">kPglRetInconsistentInput</span><span class="p">;</span></span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"> <span class="p">}</span></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="cpp"> <span class="nl">MergePsams_ret_1:</span></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp"> <span class="n" style="color: #333;">CleanupTextStream2</span><span class="p">(</span><span class="n" style="color: #333;">cur_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">txs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">reterr</span><span class="p">);</span></span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackDoubleReset</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_mark</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_end_mark</span><span class="p">);</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
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1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="cpp"><span class="p">}</span></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp"></span>
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1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">sample_sort_mode</span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">__attribute__</span><span class="p">((</span><span class="n" style="color: #333;">unused</span><span class="p">))</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_base</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bigstack_end_mark</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_bigstack_end</span><span class="p">;</span></span>
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74
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1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="cpp"> <span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetSuccess</span><span class="p">;</span></span>
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75
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="cpp"> <span class="p">{</span></span>
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76
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1. Construct/load fileset list.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); 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="1226" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -81,17 +1226,63 @@ PglErr Pmerge(__attribute__((unused)) const PmergeInfo* pmip, __attribute__((unu</td>
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81
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1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 4. If filesets cover disjoint positions, handle this as a concatenation</span></span>
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82
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1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// job (or error out on --variant-inner-join).</span></span>
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83
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5. Otherwise, perform general-purpose incremental merge.</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// const PmergeFlags flags = pmip->flags;</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="p">;;;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">filesets</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="86" style="width: 35px; color: rgba(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="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">filesets_endp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filesets</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pgenname</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocFilesetLlEntry</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filesets_endp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1233
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<pre style="margin: 0;">+<span id="LC1233" 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;">cur_entry</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" 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;">pgen_fname_blen</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;">pgenname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pvar_fname_blen</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;">pvarname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">psam_fname_blen</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;">psamname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">bigstack_end_alloc_c</span><span class="p">(</span><span class="n" style="color: #333;">pgen_fname_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pvar_fname_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">psam_fname_blen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fname_iter</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="n" style="color: #333;">pgen_fname_blen</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp"> <span class="n" style="color: #333;">fname_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="n" style="color: #333;">pvar_fname_blen</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_iter</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">fname_iter</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="n" style="color: #333;">psam_fname_blen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1250
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<pre style="margin: 0;">+<span id="LC1250" 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;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="cpp"> <span class="n" style="color: #333;">PmergeInputFilesetLl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cur_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AllocFilesetLlEntry</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filesets_endp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1252
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<pre style="margin: 0;">+<span id="LC1252" 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;">cur_entry</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_NOMEM</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pgen_fname</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pvar_fname</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_entry</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">psam_fname</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1259
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<pre style="margin: 0;">+<span id="LC1259" 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;">LoadPmergeList</span><span class="p">(</span><span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_fname</span><span class="p">,</span> <span class="n" style="color: #333;">pmip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_mode</span><span class="p">,</span> <span class="n" style="color: #333;">pgenname</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filesets_endp</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"> <span class="n" style="color: #333;">SampleIdInfo</span> <span class="n" style="color: #333;">sii</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"> <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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1267
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<pre style="margin: 0;">+<span id="LC1267" 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;">MergePsams</span><span class="p">(</span><span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">sample_sort_mode</span><span class="p">,</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">filesets</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sii</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sample_ct</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1271
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">reterr</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1273
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(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="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
</td>
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
86
</td>
<td class="diff-line-num new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1275
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --pmerge[-list] is under development.</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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
</td>
<td class="diff-line-num new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1276
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
88
</td>
<td class="diff-line-num new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1277
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Pmerge_ret_1</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
89
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<td class="diff-line-num new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1278
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
90
</td>
<td class="diff-line-num new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1279
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<td class="diff-line-num new_line old" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(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="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1280
</td>
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="nl">Pmerge_ret_NOMEM:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(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="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1281
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNomem</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(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="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1282
</td>
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
</td>
<td class="diff-line-num new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1283
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
</td>
<td class="diff-line-num new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1284
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="nl">Pmerge_ret_1:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
</td>
<td class="diff-line-num new_line old" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">Bigstack<span class="idiff left">Reset</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">bigstack</span>_mark</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1285
</td>
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">Bigstack<span class="idiff left">DoubleReset</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bigstack_mark</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bigstack_end</span>_mark</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
95
</td>
<td class="diff-line-num new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1286
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reterr</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
</td>
<td class="diff-line-num new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1287
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp"><span class="p">}</span></span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
</td>
<td class="diff-line-num new_line" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1288
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1288" class="line" lang="cpp"></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); 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="2116" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -925,7 +2116,7 @@ PglErr PgenDiff(const uintptr_t* orig_sample_include, const SampleIdInfo* siip,</td>
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925
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2116
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<pre style="margin: 0;"> <span id="LC2116" 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_max_merged_alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cur_allele_ct1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cur_allele_ct2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">allele1_alt_start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">allele2_alt_start</span><span class="p">;</span></span>
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926
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<td class="diff-line-num new_line" data-linenumber="2117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2117
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<pre style="margin: 0;"> <span id="LC2117" 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_htable_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cur_max_merged_alleles</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">9</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
927
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<td class="diff-line-num new_line" data-linenumber="2118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="cpp"> <span class="n" style="color: #333;">SetAllU32Arr</span><span class="p">(</span><span class="n" style="color: #333;">cur_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">);</span></span>
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928
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<td class="diff-line-num new_line old" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// See e.g PopulateStrboxHtable().</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// See e.g<span class="idiff left right">.</span> PopulateStrboxHtable().</span></span>
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929
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<td class="diff-line-num new_line" data-linenumber="2120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2120
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<pre style="margin: 0;"> <span id="LC2120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">);</span></span>
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930
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2121
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<pre style="margin: 0;"> <span id="LC2121" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</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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931
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2122
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<pre style="margin: 0;"> <span id="LC2122" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); 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="2127" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -936,27 +2127,18 @@ PglErr PgenDiff(const uintptr_t* orig_sample_include, const SampleIdInfo* siip,</td>
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936
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2127
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<pre style="margin: 0;"> <span id="LC2127" class="line" lang="cpp"> <span class="p">}</span></span>
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937
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2128
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<pre style="margin: 0;"> <span id="LC2128" 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_allele1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele1s</span><span class="p">[</span><span class="n" style="color: #333;">allele1_idx</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
938
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<td class="diff-line-num new_line" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2129
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<pre style="margin: 0;"> <span id="LC2129" 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_allele1_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_allele1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
939
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<td class="diff-line-num new_line old" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele1</span><span class="p">,</span> <span class="n" style="color: #333;">cur_allele1_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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940
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<td class="diff-line-num new_line old" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC940" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
941
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<td class="diff-line-num new_line old" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
942
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<td class="diff-line-num new_line old" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC942" 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;">merged_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPglMaxAlleleCt</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
943
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<td class="diff-line-num new_line old" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Too many alleles across --pgen-diff and main filesets for variant '%s' at position %s:%u. (This "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" build is limited to "</span> <span class="n" style="color: #333;">PGL_MAX_ALLELE_CT_STR</span> <span class="s" style="color: #d14;">".)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">cur_included_bp</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PgenDiff_ret_1</span><span class="p">;</span></span>
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946
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="cpp"> <span class="p">}</span></span>
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947
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">remap1</span><span class="p">[</span><span class="n" style="color: #333;">allele1_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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948
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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949
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele1</span><span class="p">;</span></span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="cpp"> <span class="p">}</span></span>
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953
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele1</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span><span class="p">],</span> <span class="n" style="color: #333;">cur_allele1_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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954
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">remap1</span><span class="p">[</span><span class="n" style="color: #333;">allele1_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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956
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="cpp"> <span class="p">}</span></span>
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957
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<pre style="margin: 0;">-<span id="LC957" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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958
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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2130
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<pre style="margin: 0;">+<span id="LC2130" 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_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele1</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles</span><span class="p">,</span> <span class="n" style="color: #333;">cur_allele1_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">);</span></span>
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2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="cpp"> <span class="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;">merged_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPglMaxAlleleCt</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Too many alleles across --pgen-diff and main filesets for variant '%s' at position %s:%u. (This "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" build is limited to "</span> <span class="n" style="color: #333;">PGL_MAX_ALLELE_CT_STR</span> <span class="s" style="color: #d14;">".)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">cur_included_bp</span><span class="p">);</span></span>
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2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PgenDiff_ret_1</span><span class="p">;</span></span>
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959
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2136
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<pre style="margin: 0;"> <span id="LC2136" class="line" lang="cpp"> <span class="p">}</span></span>
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2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="cpp"> <span class="n" style="color: #333;">remap1</span><span class="p">[</span><span class="n" style="color: #333;">allele1_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele1</span><span class="p">;</span></span>
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2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2141
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<pre style="margin: 0;">+<span id="LC2141" class="line" lang="cpp"> <span class="n" style="color: #333;">remap1</span><span class="p">[</span><span class="n" style="color: #333;">allele1_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_idx</span><span class="p">;</span></span>
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960
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2142
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<pre style="margin: 0;"> <span id="LC2142" class="line" lang="cpp"> <span class="p">}</span></span>
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961
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2143
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<pre style="margin: 0;"> <span id="LC2143" class="line" lang="cpp"> <span class="p">}</span></span>
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962
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2144
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<pre style="margin: 0;"> <span id="LC2144" 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;">allele2_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele2_alt_start</span><span class="p">;</span> <span class="n" style="color: #333;">allele2_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cur_allele_ct2</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); 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="2147" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -965,27 +2147,18 @@ PglErr PgenDiff(const uintptr_t* orig_sample_include, const SampleIdInfo* siip,</td>
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965
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2147
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<pre style="margin: 0;"> <span id="LC2147" class="line" lang="cpp"> <span class="p">}</span></span>
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966
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<td class="diff-line-num new_line" data-linenumber="2148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2148
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<pre style="margin: 0;"> <span id="LC2148" 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_allele2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele2s</span><span class="p">[</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">];</span></span>
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967
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<td class="diff-line-num new_line" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2149
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<pre style="margin: 0;"> <span id="LC2149" 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_allele2_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_allele2</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
968
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele2</span><span class="p">,</span> <span class="n" style="color: #333;">cur_allele2_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" 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;">merged_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPglMaxAlleleCt</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Too many alleles across --pgen-diff and main filesets for variant '%s' at position %s:%u. (This "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" build is limited to "</span> <span class="n" style="color: #333;">PGL_MAX_ALLELE_CT_STR</span> <span class="s" style="color: #d14;">".)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">cur_included_bp</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PgenDiff_ret_1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="cpp"> <span class="p">}</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">remap2</span><span class="p">[</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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977
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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978
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele2</span><span class="p">;</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="cpp"> <span class="p">}</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele2</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span><span class="p">],</span> <span class="n" style="color: #333;">cur_allele2_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="cpp"> <span class="n" style="color: #333;">remap2</span><span class="p">[</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"> <span class="p">}</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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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2150
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<pre style="margin: 0;">+<span id="LC2150" 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_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">cur_allele2</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles</span><span class="p">,</span> <span class="n" style="color: #333;">cur_allele2_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cur_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">,</span> <span class="n" style="color: #333;">merged_alleles_htable</span><span class="p">);</span></span>
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2151
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<pre style="margin: 0;">+<span id="LC2151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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2152
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<pre style="margin: 0;">+<span id="LC2152" class="line" lang="cpp"> <span class="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;">merged_allele_ct</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kPglMaxAlleleCt</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2153
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<pre style="margin: 0;">+<span id="LC2153" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Too many alleles across --pgen-diff and main filesets for variant '%s' at position %s:%u. (This "</span> <span class="n" style="color: #333;">PROG_NAME_STR</span> <span class="s" style="color: #d14;">" build is limited to "</span> <span class="n" style="color: #333;">PGL_MAX_ALLELE_CT_STR</span> <span class="s" style="color: #d14;">".)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">[</span><span class="n" style="color: #333;">variant_uidx</span><span class="p">],</span> <span class="n" style="color: #333;">chr_buf</span><span class="p">,</span> <span class="n" style="color: #333;">cur_included_bp</span><span class="p">);</span></span>
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2154
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<pre style="margin: 0;">+<span id="LC2154" class="line" lang="cpp"> <span class="n" style="color: #333;">reterr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kPglRetNotYetSupported</span><span class="p">;</span></span>
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2155
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">PgenDiff_ret_1</span><span class="p">;</span></span>
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988
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2156
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<pre style="margin: 0;"> <span id="LC2156" class="line" lang="cpp"> <span class="p">}</span></span>
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2157
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<pre style="margin: 0;">+<span id="LC2157" class="line" lang="cpp"> <span class="n" style="color: #333;">remap2</span><span class="p">[</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2158" class="line" lang="cpp"> <span class="n" style="color: #333;">merged_alleles</span><span class="p">[</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_allele2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2159" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2160" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2161" class="line" lang="cpp"> <span class="n" style="color: #333;">remap2</span><span class="p">[</span><span class="n" style="color: #333;">allele2_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_idx</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2162" class="line" lang="cpp"> <span class="p">}</span></span>
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2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="cpp"> <span class="p">}</span></span>
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991
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2164
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<pre style="margin: 0;"> <span id="LC2164" 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;">merged_allele_ctl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitCtToWordCt</span><span class="p">(</span><span class="n" style="color: #333;">merged_allele_ct</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#59216b3409d1d2c9ff4b9a784709ac15d3a3e12c"><strong>plink2_merge.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,15 +71,13 @@ ENUM_U31_DEF_START()</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">kMergeFilterModeNonpassUnion</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">MergeFilterMode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// this is a hybrid, only kfSortFileSid is actually a flag</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSort0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSortNone</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSortNatural</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSortAscii</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSortFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">3</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">kfSortFileSid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">SortFlags</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_START</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">kSort0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">kSortNone</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">kSortNatural</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">kSortAscii</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">kSortFile</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="n" style="color: #333;">ENUM_U31_DEF_END</span><span class="p">(</span><span class="n" style="color: #333;">SortMode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// --pgen-diff based here due to --merge-mode 6/7 history</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="n" style="color: #333;">FLAGSET_DEF_START</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,7 +108,8 @@ typedef struct PmergeStruct {</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeQualInfoMode</span> <span class="n" style="color: #333;">merge_qual_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeFilterMode</span> <span class="n" style="color: #333;">merge_filter_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">MergeQualInfoMode</span> <span class="n" style="color: #333;">merge_info_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">SortFlags</span> <span class="n" style="color: #333;">merge_info_sort</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">merge_pheno_sort</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">SortMode</span> <span class="n" style="color: #333;">merge_info_sort</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_ct</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC114" 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;">pgen_fname</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvar_fname</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,7 +134,7 @@ void InitPgenDiff(PgenDiffInfo* pgen_diff_info_ptr);</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CleanupPgenDiff</span><span class="p">(</span><span class="n" style="color: #333;">PgenDiffInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgen_diff_info_ptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">Sort<span class="idiff left">Flags</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sample_sort_flags</span></span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">Pmerge</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PmergeInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pmip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sample_sort_fname</span><span class="p">,</span> <span class="n" style="color: #333;">MiscFlags</span> <span class="n" style="color: #333;">misc_flags</span><span class="p">,</span> <span class="n" style="color: #333;">Sort<span class="idiff left">Mode</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sample_sort_mode</span></span><span class="p">,</span> <span class="n" style="color: #333;">FamCol</span> <span class="n" style="color: #333;">fam_cols</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">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;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgenname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">psamname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvarname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">);</span></span>
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139
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"></span>
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140
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"><span class="n" style="color: #333;">PglErr</span> <span class="n" style="color: #333;">PgenDiff</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig_sample_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SampleIdInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_nm</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sex_male</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_include</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ChrInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cip</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_bps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variant_ids</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_idx_offsets</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele_storage</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PgenDiffInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pdip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">orig_sample_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">raw_variant_ct</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_ct1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_allele_slen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_thread_ct</span><span class="p">,</span> <span class="n" style="color: #333;">PgenFileInfo</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pgfip</span><span class="p">,</span> <span class="n" style="color: #333;">PgenReader</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple_pgrp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">outname_end</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#68ec2c295201ac9d061fcfc37744eba392732614"><strong>plink2_misc.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">@@ -512,7 +512,7 @@ PglErr UpdateVarAlleles(const char* fname, const uintptr_t* variant_include, con</td>
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">old_allele2_match</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cur_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="n" style="color: #333;">old_slen1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">old_allele1_start</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">))</span> <span class="p">{</span></span>
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513
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<td class="diff-line-num new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="nl">UpdateVarAlleles_errfile:</span></span>
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514
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">err_ct</span><span class="p">)</span> <span class="p">{</span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="s" style="color: #d14;">".allele.no.snp"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="516" style="width: 35px; color: rgba(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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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy<span class="idiff left right">_k</span></span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="s" style="color: #d14;">".allele.no.snp"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
516
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fopen_checked</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">FOPEN_WB</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">errfile</span><span class="p">))</span> <span class="p">{</span></span>
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517
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">UpdateVarAlleles_ret_OPEN_FAIL</span><span class="p">;</span></span>
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518
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518
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<pre style="margin: 0;"> <span id="LC518" 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="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1023,7 +1023,7 @@ PglErr RecoverVarIds(const char* fname, const uintptr_t* variant_include, const</td>
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1023
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<td class="diff-line-num new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">logprintf</span><span class="p">(</span><span class="s" style="color: #d14;">"--recover-var-ids: %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" line%s scanned.</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;">line_idx</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">line_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"s"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1024
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<td class="diff-line-num new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1024
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<pre style="margin: 0;"> <span id="LC1024" 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;">conflict_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PopcountWords</span><span class="p">(</span><span class="n" style="color: #333;">conflict_bitarr</span><span class="p">,</span> <span class="n" style="color: #333;">raw_variant_ctl</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
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<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">conflict_ct</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1026
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<td class="diff-line-num new_line old" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="s" style="color: #d14;">".recoverid.dup"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1027" style="width: 35px; color: rgba(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="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">strcpy<span class="idiff left right">_k</span></span><span class="p">(</span><span class="n" style="color: #333;">outname_end</span><span class="p">,</span> <span class="s" style="color: #d14;">".recoverid.dup"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<td class="diff-line-num new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fopen_checked</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">FOPEN_WB</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">errfile</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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<td class="diff-line-num new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">RecoverVarIds_ret_OPEN_FAIL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1029
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1029
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<pre style="margin: 0;"> <span id="LC1029" 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="1290" style="width: 35px; color: rgba(0,0,0,0.3); 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="1290" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1290,33 +1290,20 @@ PglErr Plink1ClusterImport(const char* within_fname, const char* catpheno_name,</td>
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1290
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<td class="diff-line-num new_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Category names are limited to "</span> <span class="n" style="color: #333;">MAX_ID_SLEN_STR</span> <span class="s" style="color: #d14;">" characters.</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="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1291
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<td class="diff-line-num new_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink1ClusterImport_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1292
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<td class="diff-line-num new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1293
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1293" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cat_htable_size</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1294
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1294" 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;">main_token_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">main_token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1295
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1295" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1296
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1297
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1298
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</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="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1299
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1299" 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;">main_token_blen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">cat_name_write_max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cat_name_iter</span><span class="p">)))</span> <span class="p">{</span></span>
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1300
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink1ClusterImport_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1302
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1302" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cat_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_iter</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1303
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1303" class="line" lang="cpp"> <span class="n" style="color: #333;">cat_name_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">cat_name_iter</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_blen</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1304
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1304" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_names</span><span class="p">[</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nonnull_cat_ct</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_start</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1305
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1305" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonnull_cat_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1306
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1306" class="line" lang="cpp"> <span class="n" style="color: #333;">cat_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_htable_entry</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1307
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1308
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1308" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1309
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">memequal</span><span class="p">(</span><span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">cur_cat_names</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span><span class="p">],</span> <span class="n" style="color: #333;">main_token_blen</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1310
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1311
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1311" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1312
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1312" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cat_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1313
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<td class="diff-line-num new_line old" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1313" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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="1314" style="width: 35px; color: rgba(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="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cur_cat_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IdHtableAdd</span><span class="p">(</span><span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">cur_cat_names</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_slen</span><span class="p">,</span> <span class="n" style="color: #333;">cat_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">nonnull_cat_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">cat_htable</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_cat_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1314" style="width: 35px; color: rgba(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="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1295
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<pre style="margin: 0;">+<span id="LC1295" 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;">main_token_slen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span><span class="p">,</span> <span class="n" style="color: #333;">cat_name_write_max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cat_name_iter</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1314" style="width: 35px; color: rgba(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="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink1ClusterImport_ret_NOMEM</span><span class="p">;</span></span>
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1314
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<td class="diff-line-num new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1315" style="width: 35px; color: rgba(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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1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cat_name_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_iter</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="cpp"> <span class="n" style="color: #333;">cat_name_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">memcpya</span><span class="p">(</span><span class="n" style="color: #333;">cat_name_iter</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_start</span><span class="p">,</span> <span class="n" style="color: #333;">main_token_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonnull_cat_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_cat_names</span><span class="p">[</span><span class="n" style="color: #333;">cur_cat_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cat_name_start</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1315
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1316
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<td class="diff-line-num new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// permit duplicates if category is identical</span></span>
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<td class="diff-line-num old_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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<td class="diff-line-num new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<pre style="margin: 0;"> <span id="LC1304" 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;">already_seen</span><span class="p">,</span> <span class="n" style="color: #333;">lb_idx</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1318
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<td class="diff-line-num new_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1305
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<pre style="margin: 0;"> <span id="LC1305" 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;">existing_cat_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sorted_cat_idxs</span><span class="p">[</span><span class="n" style="color: #333;">lb_idx</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1319
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<td class="diff-line-num new_line old" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1319" 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;">existing_cat_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cur_<span class="idiff left right">htable_entry</span></span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1320" style="width: 35px; color: rgba(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="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" 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;">existing_cat_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cur_<span class="idiff left right">cat_idx</span></span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1320
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<td class="diff-line-num new_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="cpp"> <span class="n" style="color: #333;">idbuf</span><span class="p">[</span><span class="n" style="color: #333;">fid_slen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">' '</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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<td class="diff-line-num new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">logpreprintfww</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Duplicate sample ID '%s' with conflicting category assignments in --within file.</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;">idbuf</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1322
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink1ClusterImport_ret_MALFORMED_INPUT_2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); 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="1312" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1325,7 +1312,7 @@ PglErr Plink1ClusterImport(const char* within_fname, const char* catpheno_name,</td>
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1325
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<td class="diff-line-num new_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1312
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<pre style="margin: 0;"> <span id="LC1312" 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="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1326
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<td class="diff-line-num new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="cpp"> <span class="n" style="color: #333;">SetBit</span><span class="p">(</span><span class="n" style="color: #333;">lb_idx</span><span class="p">,</span> <span class="n" style="color: #333;">already_seen</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<td class="diff-line-num new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">lb_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ub_idx</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">lb_idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1328
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<td class="diff-line-num new_line old" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1328" class="line" lang="cpp"> <span class="n" style="color: #333;">sorted_cat_idxs</span><span class="p">[</span><span class="n" style="color: #333;">lb_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_<span class="idiff left right">htable_entry</span></span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1329" style="width: 35px; color: rgba(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="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="cpp"> <span class="n" style="color: #333;">sorted_cat_idxs</span><span class="p">[</span><span class="n" style="color: #333;">lb_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_<span class="idiff left right">cat_idx</span></span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1329
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<td class="diff-line-num new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1330
</td>
<td class="diff-line-num new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1331
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1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">Plink1ClusterImport_LINE_ITER_ALREADY_ADVANCED</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); 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="1923" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1936,6 +1923,10 @@ PglErr UpdateSampleIds(const char* fname, const uintptr_t* sample_include, uint3</td>
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1936
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<td class="diff-line-num new_line" data-linenumber="1923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1923
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<pre style="margin: 0;"> <span id="LC1923" 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="1937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1937
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<td class="diff-line-num new_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1924
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="cpp"> <span class="n" style="color: #333;">xid_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_sid_present</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">kfXidModeIidSid</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">kfXidModeIid</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1938
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<td class="diff-line-num new_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1925
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">new_fid_present</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1939" style="width: 35px; color: rgba(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="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (14 Jan 2021)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1939" style="width: 35px; color: rgba(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="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="cpp"> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">kfSampleIdFidPresent</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1939" style="width: 35px; color: rgba(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="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="cpp"> <span class="p">}</span></span>
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1939
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1930
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<pre style="margin: 0;"> <span id="LC1930" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sample_id_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sample_id_blen</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1940
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<td class="diff-line-num new_line" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">max_sid_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_sid_blen</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1941
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<td class="diff-line-num new_line" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1932
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<pre style="margin: 0;"> <span id="LC1932" 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;">xid_map</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="9007" style="width: 35px; color: rgba(0,0,0,0.3); 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="8998" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9007,19 +8998,9 @@ PglErr WriteCovar(const uintptr_t* sample_include, const PedigreeIdInfo* piip, c</td>
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<td class="diff-line-num old_line" data-linenumber="9007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9007
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<td class="diff-line-num new_line" data-linenumber="8998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8998
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<pre style="margin: 0;"> <span id="LC8998" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_xcovar_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_covar_name_blen</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9008
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<td class="diff-line-num new_line" data-linenumber="8999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8999
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<pre style="margin: 0;"> <span id="LC8999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">write_sex</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9009
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<td class="diff-line-num new_line" data-linenumber="9000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9000
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<pre style="margin: 0;"> <span id="LC9000" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add "SEX"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9010
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9010" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="s" style="color: #d14;">"SEX"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">covar_name_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9011
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9011" 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_htable_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covar_name_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9012
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9012" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9013
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9013" class="line" lang="cpp"> <span class="n" style="color: #333;">covar_name_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covar_ct</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9014
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9014" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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9015
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<pre style="margin: 0;">-<span id="LC9015" class="line" lang="cpp"> <span class="p">}</span></span>
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9016
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9016" 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;">strequal_k_unsafe</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">covar_names</span><span class="p">[</span><span class="n" style="color: #333;">cur_htable_entry</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_covar_name_blen</span><span class="p">]),</span> <span class="s" style="color: #d14;">"SEX"</span><span class="p">)))</span> <span class="p">{</span></span>
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9017
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9017" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: .cov file cannot have both a regular SEX column and a covariate named</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'SEX'. Exclude or rename one of these columns.</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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9018
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9018" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WriteCovar_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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9019
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9019" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9020
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9020" 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;">hashval</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">covar_name_htable_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9021
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9021" class="line" lang="cpp"> <span class="n" style="color: #333;">hashval</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="9022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9022
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<td class="diff-line-num new_line old" data-linenumber="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9022" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9023" style="width: 35px; color: rgba(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="9001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9001
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<pre style="margin: 0;">+<span id="LC9001" 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;">StrboxHtableAdd</span><span class="p">(</span><span class="s" style="color: #d14;">"SEX"</span><span class="p">,</span> <span class="n" style="color: #333;">covar_names</span><span class="p">,</span> <span class="n" style="color: #333;">max_covar_name_blen</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"SEX"</span><span class="p">),</span> <span class="n" style="color: #333;">covar_name_htable_size</span><span class="p">,</span> <span class="n" style="color: #333;">covar_ct</span><span class="p">,</span> <span class="n" style="color: #333;">covar_name_htable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9002
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<pre style="margin: 0;">+<span id="LC9002" class="line" lang="cpp"> <span class="n" style="color: #333;">logerrputs</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: .cov file cannot have both a regular SEX column and a covariate named</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'SEX'. Exclude or rename one of these columns.</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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9003
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<pre style="margin: 0;">+<span id="LC9003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">WriteCovar_ret_INCONSISTENT_INPUT</span><span class="p">;</span></span>
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9023
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9004
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<pre style="margin: 0;"> <span id="LC9004" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="9024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9024
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<td class="diff-line-num new_line" data-linenumber="9005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9005
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<pre style="margin: 0;"> <span id="LC9005" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">max_xcovar_name_blen</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 old_line" data-linenumber="9025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9025
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9006
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<pre style="margin: 0;"> <span id="LC9006" class="line" lang="cpp"> <span class="n" style="color: #333;">max_xcovar_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9031" style="width: 35px; color: rgba(0,0,0,0.3); 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="9012" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9031,6 +9012,8 @@ PglErr WriteCovar(const uintptr_t* sample_include, const PedigreeIdInfo* piip, c</td>
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9031
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<td class="diff-line-num new_line" data-linenumber="9012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9012
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<pre style="margin: 0;"> <span id="LC9012" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">write_iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9032
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<td class="diff-line-num new_line" data-linenumber="9013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9013
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<pre style="margin: 0;"> <span id="LC9013" 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_pheno_name_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;">pheno_name_iter</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="9033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9033
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<td class="diff-line-num new_line" data-linenumber="9014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9014
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<pre style="margin: 0;"> <span id="LC9014" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cur_pheno_name_slen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_xcovar_name_blen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9034" style="width: 35px; color: rgba(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="9015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9015
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<pre style="margin: 0;">+<span id="LC9015" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// can't just use StrboxHtableFind() since "SEX" may not be stored</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9034" style="width: 35px; color: rgba(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="9016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9016
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<pre style="margin: 0;">+<span id="LC9016" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// in covar_names[]</span></span>
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9034
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<td class="diff-line-num new_line" data-linenumber="9017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9017
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<pre style="margin: 0;"> <span id="LC9017" 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_pheno_name_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_pheno_name_slen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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9035
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9018
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<pre style="margin: 0;"> <span id="LC9018" 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;">hashval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashceil</span><span class="p">(</span><span class="n" style="color: #333;">pheno_name_iter</span><span class="p">,</span> <span class="n" style="color: #333;">cur_pheno_name_slen</span><span class="p">,</span> <span class="n" style="color: #333;">covar_name_htable_size</span><span class="p">);</span> <span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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9036
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9019
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<pre style="margin: 0;"> <span id="LC9019" 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_htable_idval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covar_name_htable</span><span class="p">[</span><span class="n" style="color: #333;">hashval</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#436d5ebb95c2149ac987678ddff33cffca2ea965"><strong>plink2_psam.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">@@ -94,7 +94,7 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parse header</span></span>
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95
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [-1] = #FID (if present, must be first column)</span></span>
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96
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [0] = IID (could also be first column)</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [1] = SID</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [1] = SID<span class="idiff left right"> (if present, must immediately follow IID)</span></span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [2] = PAT</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [3] = MAT</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// [4] = SEX</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">@@ -229,7 +229,15 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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229
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="p">}</span></span>
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230
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">BigstackBaseSet</span><span class="p">(</span><span class="n" style="color: #333;">ll_alloc_base</span><span class="p">);</span></span>
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231
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231
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<pre style="margin: 0;"> <span id="LC231" 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;">psam_cols_mask</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="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
232
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<pre style="margin: 0;">-<span id="LC232" 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: No IID column on line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of %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;">line_idx</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">);</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" 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: No IID column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">);</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="p">}</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" 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;">col_types</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;">0</span><span class="p">))</span> <span class="p">{</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: IID column is not first or second in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">((</span><span class="n" style="color: #333;">psam_cols_mask</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">col_types</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">col_skips</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: SID column does not immediately follow IID column in %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">psamname</span><span class="p">);</span></span>
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233
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">LoadPsam_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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234
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="p">}</span></span>
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235
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">in_interval</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); 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="265" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -257,7 +265,7 @@ PglErr LoadPsam(const char* psamname, const RangeList* pheno_range_list_ptr, Fam</td>
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257
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<td class="diff-line-num new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw_rd</span><span class="p">(</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)));</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">bigstack_alloc_raw_rd</span><span class="p">(</span><span class="n" style="color: #333;">relevant_postfid_col_ct</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)));</span></span>
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259
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">bigstack_mark2</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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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</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;">f<span class="idiff left">am_cols</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="c1" style="color: #998; font-style: italic;"><span class="idiff right">// assumes kfFamCol1 == 1</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="261" style="width: 35px; color: rgba(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="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">col_skips</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;">f<span class="idiff left">id_present</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
261
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">col_types</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;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
262
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// psam_cols_mask = 1; // may need this later</span></span>
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<td class="diff-line-num old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
263
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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">rpf_col_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<li id="c213d6a8351bbee48c82c7a6399fd1202e28bf94">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/b3bdaa5c97903f7ddb36c6cf575f8de04699552d#c213d6a8351bbee48c82c7a6399fd1202e28bf94"><strong>plink2_psam.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -35,8 +35,8 @@ namespace plink2 {</td>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// by a leading '#'. All lines which don't start with '#FID' or '#IID' are</span></span>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// currently ignored. The #FID/IID line specifies the columns in the .psam</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// file; the following column headers are recognized:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// IID (required)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SID</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// IID (required<span class="idiff left right">, must be first or second</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SID<span class="idiff left right"> (must immediately follow IID if present)</span></span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// PAT</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// MAT</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SEX</span></span>
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