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<h3>

Dylan Aïssi pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/plink1-9">Debian Med / plink1.9</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/3dad9748b246b0b83a98c88d010959ae5ceb34ce">3dad9748</a></strong>

<div>

<span>by Dylan Aïssi</span>

<i>at 2020-07-06T15:46:21+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.18-200616</pre>

</li>

</ul>

<h4>3 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">

plink.c

</a>

</li>

<li class="file-stats">

<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">

plink_data.c

</a>

</li>

<li class="file-stats">

<a href="#ad63a8112365845088935bd1cf043fd5464ed840">

plink_misc.c

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">

<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/3dad9748b246b0b83a98c88d010959ae5ceb34ce#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,7 +93,7 @@</td>

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93

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90b6.1<span class="idiff left right">7</span>"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90b6.1<span class="idiff left right">8</span>"</span></span>

</pre>

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<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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">  <span class="s" style="color: #d14;">"PLINK v1.90p"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="105" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -105,7 +105,7 @@ static const char ver_str[] =</td>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c">  <span class="s" style="color: #d14;">" 32-bit"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c">  <span class="s" style="color: #d14;">" (<span class="idiff left right">28 Apr</span> 2020)"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c">  <span class="s" style="color: #d14;">" (<span class="idiff left right">16 Jun</span> 2020)"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c">  <span class="s" style="color: #d14;">""</span></span>

</pre>

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<br>

</li>

<li id="f101da6685d6d3284ff66b606e058f55eebde6b7">

<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/3dad9748b246b0b83a98c88d010959ae5ceb34ce#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.c</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">@@ -15067,7 +15067,7 @@ int32_t report_non_biallelics(char* outname, char* outname_end, Ll_str* non_bial</td>

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<pre style="margin: 0;"> <span id="LC15067" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fclose_null</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="15068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15068" class="line" lang="c">    <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">report_non_biallelics_ret_WRITE_FAIL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC15069" class="line" lang="c">  <span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="15070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="15070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15070" class="line" lang="c">  <span class="n" style="color: #333;">LOGERRPRINTF</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" variant%s with 3+ alleles present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">* If you believe this is due to strand inconsistency, try --flip with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  (Warning: if this seems to work, strand errors involving SNPs with A/T or C/G</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  alleles probably remain in your data.  If LD between nearby SNPs is high,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  --flip-scan should detect them.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">* If you are dealing with genuine multiallelic variants, we recommend exporting</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  that subset of the data to VCF (via e.g. '--recode vcf'), merging with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  another tool/script, and then importing the result; PLINK is not yet suited</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  to handling them.</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;">nbmarker_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">nbmarker_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;">outname</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="15071" style="width: 35px; color: rgba(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="15070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15070

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<pre style="margin: 0;">+<span id="LC15070" class="line" lang="c">  <span class="n" style="color: #333;">LOGERRPRINTF</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" variant%s with 3+ alleles present.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">* If you believe this is due to strand inconsistency, try --flip with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  (Warning: if this seems to work, strand errors involving SNPs with A/T or C/G</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  alleles probably remain in your data.  If LD between nearby SNPs is high,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  --flip-scan should detect them.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">* If you are dealing with genuine multiallelic variants, we recommend exporting</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  that subset of the data to VCF (via e.g. '--recode vcf'), merging with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  another tool/script, and then importing the result; PLINK is not yet suited</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">  to handling them.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"><span class="idiff left">See https://www.cog-genomics.org/plink/1.9/data#merge3 for more discussion.</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nbmarker_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">nbmarker_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;">outname</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="15071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15071" class="line" lang="c">  <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_line" data-linenumber="15072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15072" class="line" lang="c">  <span class="nl">report_non_biallelics_ret_NOMEM:</span></span>

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<pre style="margin: 0;"> <span id="LC15073" class="line" lang="c">    <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RET_NOMEM</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16452" style="width: 35px; color: rgba(0,0,0,0.3); 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="16452" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -16452,6 +16452,24 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>

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<pre style="margin: 0;"> <span id="LC16452" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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_line" data-linenumber="16453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16453" class="line" lang="c">      <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC16454" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC16455" class="line" lang="c">    <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;">mlpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ullxx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cur_marker_ct</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC16456" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// Update (2 May 2020): PLINK 1.07 errored out if the first input fileset</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16457" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// had two variants with the same ID.  However, it did *not* do so if</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16458" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// this was true of later filesets, so in cases like</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16459" style="width: 35px; color: rgba(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="LC16459" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//   https://github.com/chrchang/plink-ng/issues/140</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16460" style="width: 35px; color: rgba(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="LC16460" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// where one but not all filesets had a duplicate ID, it would behave in</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16461" style="width: 35px; color: rgba(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="LC16461" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// an asymmetric manner.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16462" style="width: 35px; color: rgba(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="LC16462" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// There are valid reasons for permitting duplicate IDs in the first</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16463" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// fileset (e.g. there are redundant loci for quality control purposes),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16464" style="width: 35px; color: rgba(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="LC16464" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// so we don't want to copy PLINK 1.07's error-out behavior.  However,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16465" style="width: 35px; color: rgba(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="LC16465" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// there are also common dangers (e.g. there are a whole bunch of</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16466" style="width: 35px; color: rgba(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="LC16466" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// variants with ID=. which should be assigned distinct IDs before</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16467" style="width: 35px; color: rgba(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="LC16467" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// merge), so printing a warning where there previously was an error is</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16468" style="width: 35px; color: rgba(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="LC16468" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// justified.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16469" style="width: 35px; color: rgba(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="LC16469" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// (Obvious todo for PLINK 2.0: also print this warning if the first</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16470" style="width: 35px; color: rgba(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="LC16470" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// fileset doesn't have a duplicate ID, but a later fileset does.)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16471" style="width: 35px; color: rgba(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="LC16471" class="line" lang="c">      <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: First fileset to be merged contains duplicate variant ID(s).  Variants</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">with matching IDs are all merged together; if this is not what you want (e.g.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">you have a bunch of novel variants, all with ID </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">), assign distinct IDs to</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">them (with e.g. --set-missing-var-ids) before rerunning this merge.</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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<pre style="margin: 0;">+<span id="LC16472" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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16455

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<pre style="margin: 0;"> <span id="LC16473" class="line" lang="c">    <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;">merge_list</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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16456

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<td class="diff-line-num new_line" data-linenumber="16474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16474

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<pre style="margin: 0;"> <span id="LC16474" class="line" lang="c">      <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;">mlpos</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16457

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<td class="diff-line-num new_line" data-linenumber="16475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16475

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<pre style="margin: 0;"> <span id="LC16475" class="line" lang="c">  <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ullxx</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16460" style="width: 35px; color: rgba(0,0,0,0.3); 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="16478" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -16460,8 +16478,6 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>

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<td class="diff-line-num old_line" data-linenumber="16460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16460

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<td class="diff-line-num new_line" data-linenumber="16478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16478

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<pre style="margin: 0;"> <span id="LC16478" class="line" lang="c">  <span class="n" style="color: #333;">LOGPRINTFWW</span><span class="p">(</span><span class="s" style="color: #d14;">"%u marker%s to be merged from %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_marker_ct</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">cur_marker_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;">mergelist_bim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16461

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<td class="diff-line-num new_line" data-linenumber="16479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16479

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<pre style="margin: 0;"> <span id="LC16479" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// bugfix: don't underflow when a single file has duplicate IDs (e.g.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16462

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<td class="diff-line-num new_line" data-linenumber="16480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16480

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<pre style="margin: 0;"> <span id="LC16480" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// '.').</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16463

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<td class="diff-line-num new_line old" data-linenumber="16481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16463" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// Merging should fail anyway in that case, but we should not embarrass</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16464

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<td class="diff-line-num new_line old" data-linenumber="16481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16464" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">// ourselves by printing inaccurate numbers here.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16465

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<td class="diff-line-num new_line" data-linenumber="16481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16481

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<pre style="margin: 0;"> <span id="LC16481" class="line" lang="c">  <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ullxx</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">uii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16466

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<td class="diff-line-num new_line" data-linenumber="16482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16482

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<pre style="margin: 0;"> <span id="LC16482" class="line" lang="c">  <span class="n" style="color: #333;">LOGPRINTF</span><span class="p">(</span><span class="s" style="color: #d14;">"Of these, %u %s new, while %u %s present in the base dataset.</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;">uii</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"is"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"are"</span><span class="p">,</span> <span class="n" style="color: #333;">cur_marker_ct</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 class="n" style="color: #333;">cur_marker_ct</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"is"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"are"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16483

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<pre style="margin: 0;"> <span id="LC16483" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="ad63a8112365845088935bd1cf043fd5464ed840">

<a href="https://salsa.debian.org/med-team/plink1-9/-/commit/3dad9748b246b0b83a98c88d010959ae5ceb34ce#ad63a8112365845088935bd1cf043fd5464ed840"><strong>plink_misc.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3725,6 +3725,7 @@ int32_t het_report(FILE* bedfile, uintptr_t bed_offset, char* outname, char* out</td>

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<td class="diff-line-num old_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3725

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<td class="diff-line-num new_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3725

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<pre style="margin: 0;"> <span id="LC3725" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">nei_sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3726

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<td class="diff-line-num new_line" data-linenumber="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3726

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<pre style="margin: 0;"> <span id="LC3726" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrom_fo_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0xffffffffU</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// deliberate overflow</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3727

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<td class="diff-line-num new_line" data-linenumber="3727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3727

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<pre style="margin: 0;"> <span id="LC3727" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrom_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3728" style="width: 35px; color: rgba(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="3728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3728

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<pre style="margin: 0;">+<span id="LC3728" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mt_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">xymt_codes</span><span class="p">[</span><span class="n" style="color: #333;">MT_OFFSET</span><span class="p">];</span></span>

</pre>

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3728

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<pre style="margin: 0;"> <span id="LC3729" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">retval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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3729

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<td class="diff-line-num new_line" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3730

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<pre style="margin: 0;"> <span id="LC3730" class="line" lang="c">  <span class="n" style="color: #333;">Pigz_state</span> <span class="n" style="color: #333;">ps</span><span class="p">;</span></span>

</pre>

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3730

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<td class="diff-line-num new_line" data-linenumber="3731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3731

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<pre style="margin: 0;"> <span id="LC3731" class="line" lang="c">  <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;">loadbuf_raw</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3799" style="width: 35px; color: rgba(0,0,0,0.3); 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="3800" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3799,9 +3800,17 @@ int32_t het_report(FILE* bedfile, uintptr_t bed_offset, char* outname, char* out</td>

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3799

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<td class="diff-line-num new_line" data-linenumber="3800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3800

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<pre style="margin: 0;"> <span id="LC3800" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3801" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">chrom_end</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3801

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<td class="diff-line-num new_line" data-linenumber="3802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3802

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<pre style="margin: 0;"> <span id="LC3802" class="line" lang="c">      <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3803" style="width: 35px; color: rgba(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="LC3803" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3802

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<td class="diff-line-num new_line" data-linenumber="3804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3804

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<pre style="margin: 0;"> <span id="LC3804" class="line" lang="c">   <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3805

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<pre style="margin: 0;"> <span id="LC3805" class="line" lang="c">     <span class="n" style="color: #333;">chrom_fo_idx</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3804

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<td class="diff-line-num new_line old" data-linenumber="3806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3804" class="line" lang="c">   <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">is_set</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_file_order</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3805" style="width: 35px; color: rgba(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="3806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3806

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<pre style="margin: 0;">+<span id="LC3806" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// bugfix (16 Jun 2020): forgot to separately exclude chrM here.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3805" style="width: 35px; color: rgba(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="3807" style="width: 35px; color: rgba(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="LC3807" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// Fortunately, this frequently didn't matter, since chrM is usually</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3808" style="width: 35px; color: rgba(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="LC3808" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// sorted last: in that case, if no alternate contigs are present,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3805" style="width: 35px; color: rgba(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="3809" style="width: 35px; color: rgba(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="LC3809" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// the marker_ct loop termination condition prevents chrM from being</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3810" style="width: 35px; color: rgba(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="LC3810" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// included.  But chrM is positioned first in some files, in which</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3805" style="width: 35px; color: rgba(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="3811" style="width: 35px; color: rgba(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="LC3811" class="line" lang="c">          <span class="c1" style="color: #998; font-style: italic;">// case this fix matters.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3812" style="width: 35px; color: rgba(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="LC3812" class="line" lang="c">          <span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_file_order</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3813" style="width: 35px; color: rgba(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="LC3813" class="line" lang="c">   <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">is_set</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">haploid_mask</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_idx</span> <span class="o" style="font-weight: 600;">==</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;">mt_code</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3805

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<td class="diff-line-num new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3814

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<pre style="margin: 0;"> <span id="LC3814" class="line" lang="c">   <span class="n" style="color: #333;">chrom_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3806

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<td class="diff-line-num new_line" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3815

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<pre style="margin: 0;"> <span id="LC3815" class="line" lang="c">   <span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_unset</span><span class="p">(</span><span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrom_fo_vidx_start</span><span class="p">[</span><span class="n" style="color: #333;">chrom_fo_idx</span><span class="p">],</span> <span class="n" style="color: #333;">chrom_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3807

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<td class="diff-line-num new_line" data-linenumber="3816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3816

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<pre style="margin: 0;"> <span id="LC3816" class="line" lang="c">      <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">marker_uidx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">chrom_end</span><span class="p">);</span></span>

</pre>

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