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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/152a5d351c04e300680727ddc3ff5e1b5c2d946a">152a5d35</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-12-15T08:16:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.13-191130</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="#faf97f9bea161b0e5da5eb07694fa31a6450cec2">
plink_help.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
<a href="https://salsa.debian.org/med-team/plink1-9/commit/152a5d351c04e300680727ddc3ff5e1b5c2d946a#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</strong></a>
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<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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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>
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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">
94
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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">
94
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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>
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95
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95
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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>
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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">2</span>"</span></span>
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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">3</span>"</span></span>
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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>
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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">
98
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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">
98
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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>
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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>
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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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105
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<td class="diff-line-num 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">
105
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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>
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106
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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>
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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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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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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 Oct</span> 2019)"</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="c"> <span class="s" style="color: #d14;">" (<span class="idiff left right">30 Nov</span> 2019)"</span><span class="p">;</span></span>
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109
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109
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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>
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110
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110
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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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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4720" style="width: 35px; color: rgba(0,0,0,0.3); 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="4720" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4720,7 +4720,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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4720
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4720
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<pre style="margin: 0;"> <span id="LC4720" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">param_ct</span><span class="p">;</span> <span class="n" style="color: #333;">uii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4721
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4721
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<pre style="margin: 0;"> <span id="LC4721" 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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uii</span><span class="p">],</span> <span class="s" style="color: #d14;">"perm"</span><span class="p">))</span> <span class="p">{</span></span>
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4722
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<td class="diff-line-num new_line" data-linenumber="4722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4722
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<pre style="margin: 0;"> <span id="LC4722" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CLUSTER_CMH_MPERM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4723
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<td class="diff-line-num new_line old" data-linenumber="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4723" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">{,-bd}</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4724" style="width: 35px; color: rgba(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="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4723
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<pre style="margin: 0;">+<span id="LC4723" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">[-bd]</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4724
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<td class="diff-line-num new_line" data-linenumber="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4724
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<pre style="margin: 0;"> <span id="LC4724" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4725
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<td class="diff-line-num new_line" data-linenumber="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4725
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<pre style="margin: 0;"> <span id="LC4725" class="line" lang="c"> <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;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM_BD</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4726
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<td class="diff-line-num new_line" data-linenumber="4726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4726
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<pre style="margin: 0;"> <span id="LC4726" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'perm' and 'perm-bd' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4729" style="width: 35px; color: rgba(0,0,0,0.3); 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="4729" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4729,7 +4729,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="4729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4729
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<td class="diff-line-num new_line" data-linenumber="4729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4729
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4729" class="line" lang="c"> <span class="n" style="color: #333;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4730
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<td class="diff-line-num new_line" data-linenumber="4730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4730
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<pre style="margin: 0;"> <span id="LC4730" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uii</span><span class="p">],</span> <span class="s" style="color: #d14;">"perm-bd"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4731
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<td class="diff-line-num new_line" data-linenumber="4731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4731
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4731" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CLUSTER_CMH_MPERM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4732
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<td class="diff-line-num new_line old" data-linenumber="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4732" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">{,-bd}</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4733" style="width: 35px; color: rgba(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="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4732
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<pre style="margin: 0;">+<span id="LC4732" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">[-bd]</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4733
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<td class="diff-line-num new_line" data-linenumber="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4733
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<pre style="margin: 0;"> <span id="LC4733" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4734
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<td class="diff-line-num new_line" data-linenumber="4734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4734
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<pre style="margin: 0;"> <span id="LC4734" class="line" lang="c"> <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;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">CLUSTER_CMH_PERM</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM_BD</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4735
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<td class="diff-line-num new_line" data-linenumber="4735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4735
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4735" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'perm' and 'perm-bd' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4741" style="width: 35px; color: rgba(0,0,0,0.3); 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="4741" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4741,7 +4741,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="4741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4741
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<td class="diff-line-num new_line" data-linenumber="4741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4741
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<pre style="margin: 0;"> <span id="LC4741" class="line" lang="c"> <span class="n" style="color: #333;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM_BD</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4742
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<td class="diff-line-num new_line" data-linenumber="4742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4742
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<pre style="margin: 0;"> <span id="LC4742" class="line" lang="c"> <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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uii</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">6</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;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">uii</span><span class="p">],</span> <span class="s" style="color: #d14;">"mperm="</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4743
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<td class="diff-line-num new_line" data-linenumber="4743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4743
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<pre style="margin: 0;"> <span id="LC4743" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CLUSTER_CMH_PERM</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4744
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<pre style="margin: 0;">-<span id="LC4744" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">{,-bd}</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4744
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<pre style="margin: 0;">+<span id="LC4744" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --bd 'mperm' and 'perm<span class="idiff left right">[-bd]</span>' cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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4745
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4745
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<pre style="margin: 0;"> <span id="LC4745" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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4746
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4746
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<pre style="margin: 0;"> <span id="LC4746" class="line" lang="c"> <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;">cluster</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CLUSTER_CMH_MPERM</span><span class="p">)</span> <span class="p">{</span></span>
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4747
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4747
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<pre style="margin: 0;"> <span id="LC4747" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Duplicate --bd 'mperm' modifier.</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 unfold js-unfold old_line" data-linenumber="4959" style="width: 35px; color: rgba(0,0,0,0.3); 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="4959" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4959,7 +4959,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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4959
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<td class="diff-line-num new_line" data-linenumber="4959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4959
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<pre style="margin: 0;"> <span id="LC4959" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="4960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4960
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4960
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<pre style="margin: 0;"> <span id="LC4960" 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;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argptr2</span><span class="p">,</span> <span class="s" style="color: #d14;">"hr"</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 old_line" data-linenumber="4961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4961
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<td class="diff-line-num new_line" data-linenumber="4961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4961
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<pre style="margin: 0;"> <span id="LC4961" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_flag_present</span><span class="p">)</span> <span class="p">{</span></span>
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4962
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<td class="diff-line-num new_line old" data-linenumber="4962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4962" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --chr cannot be used with --autosome<span class="idiff left right">{,-xy}</span>.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4963" style="width: 35px; color: rgba(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="4962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4962
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<pre style="margin: 0;">+<span id="LC4962" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --chr cannot be used with --autosome<span class="idiff left right">[-xy]</span>.</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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4963
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4963
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<pre style="margin: 0;"> <span id="LC4963" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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4964
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4964
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<pre style="margin: 0;"> <span id="LC4964" class="line" lang="c"> <span class="p">}</span></span>
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4965
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4965
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<pre style="margin: 0;"> <span id="LC4965" 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;">parse_chrom_ranges</span><span class="p">(</span><span class="n" style="color: #333;">param_ct</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span><span class="p">]),</span> <span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">chrom_mask</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrom_info</span><span class="p">,</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;">MISC_ALLOW_EXTRA_CHROMS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">argptr</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6680" style="width: 35px; color: rgba(0,0,0,0.3); 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="6680" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6680,7 +6680,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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6680
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6680
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<pre style="margin: 0;"> <span id="LC6680" class="line" lang="c"> <span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">MISC_FREQX</span><span class="p">;</span></span>
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6681
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6681
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<pre style="margin: 0;"> <span id="LC6681" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argptr2</span><span class="p">,</span> <span class="s" style="color: #d14;">"rom"</span><span class="p">,</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="6682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6682
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6682
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<pre style="margin: 0;"> <span id="LC6682" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrom_flag_present</span><span class="p">)</span> <span class="p">{</span></span>
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6683
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<td class="diff-line-num new_line old" data-linenumber="6683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6683" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --from cannot be used with --autosome<span class="idiff left right">{,-xy} or --{,not-}</span>chr.</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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6683
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<pre style="margin: 0;">+<span id="LC6683" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --from cannot be used with --autosome<span class="idiff left right">[-xy] or --[not-]</span>chr.</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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6684
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6684
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<pre style="margin: 0;"> <span id="LC6684" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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6685
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6685
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<pre style="margin: 0;"> <span id="LC6685" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="6686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6686
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6686
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<pre style="margin: 0;"> <span id="LC6686" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">enforce_param_ct_range</span><span class="p">(</span><span class="n" style="color: #333;">param_ct</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9593" style="width: 35px; color: rgba(0,0,0,0.3); 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="9593" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9593,7 +9593,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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9593
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<td class="diff-line-num new_line" data-linenumber="9593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9593
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<pre style="margin: 0;"> <span id="LC9593" class="line" lang="c"> <span class="n" style="color: #333;">calculation_type</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">CALC_NEIGHBOR</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9594
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<td class="diff-line-num new_line" data-linenumber="9594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9594
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<pre style="margin: 0;"> <span id="LC9594" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argptr2</span><span class="p">,</span> <span class="s" style="color: #d14;">"ot-chr"</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9595
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<td class="diff-line-num new_line" data-linenumber="9595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9595
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<pre style="margin: 0;"> <span id="LC9595" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">markername_from</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9596
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<td class="diff-line-num new_line old" data-linenumber="9596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9596" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --from cannot be used with --autosome<span class="idiff left right">{,-xy} or --{,not-}</span>chr.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9597" style="width: 35px; color: rgba(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="9596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9596
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<pre style="margin: 0;">+<span id="LC9596" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --from cannot be used with --autosome<span class="idiff left right">[-xy] or --[not-]</span>chr.</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="9597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9597
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<td class="diff-line-num new_line" data-linenumber="9597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9597
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<pre style="margin: 0;"> <span id="LC9597" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9598
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9598
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<pre style="margin: 0;"> <span id="LC9598" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="9599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9599
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9599
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<pre style="margin: 0;"> <span id="LC9599" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// allowed:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9603" style="width: 35px; color: rgba(0,0,0,0.3); 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="9603" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9603,7 +9603,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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9603
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<td class="diff-line-num new_line" data-linenumber="9603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9603
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<pre style="margin: 0;"> <span id="LC9603" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// does not make sense, disallowed:</span></span>
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<td class="diff-line-num old_line" data-linenumber="9604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9604
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<td class="diff-line-num new_line" data-linenumber="9604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9604
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<pre style="margin: 0;"> <span id="LC9604" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr --chr 5-22 --not-chr bobs_chrom</span></span>
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<td class="diff-line-num old_line" data-linenumber="9605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9605
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9605
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<pre style="margin: 0;"> <span id="LC9605" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="9606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9606
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<td class="diff-line-num new_line old" data-linenumber="9606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9606" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr present, --chr/--autosome<span class="idiff left right">{,-xy}</span> not present</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9607" style="width: 35px; color: rgba(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="9606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9606
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<pre style="margin: 0;">+<span id="LC9606" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// --allow-extra-chr present, --chr/--autosome<span class="idiff left right">[-xy]</span> not present</span></span>
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9607
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9607
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<pre style="margin: 0;"> <span id="LC9607" class="line" lang="c"> <span class="n" style="color: #333;">uii</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">misc_flags</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">MISC_ALLOW_EXTRA_CHROMS</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">is_include_stack</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="9608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9608
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<td class="diff-line-num new_line" data-linenumber="9608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9608
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<pre style="margin: 0;"> <span id="LC9608" 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;">parse_chrom_ranges</span><span class="p">(</span><span class="n" style="color: #333;">param_ct</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cur_arg</span><span class="p">]),</span> <span class="n" style="color: #333;">chrom_exclude</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrom_info</span><span class="p">,</span> <span class="n" style="color: #333;">uii</span><span class="p">,</span> <span class="n" style="color: #333;">argptr</span><span class="p">);</span></span>
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9609
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9609
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<pre style="margin: 0;"> <span id="LC9609" 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 unfold js-unfold new_line" data-linenumber="9870" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9870,13 +9870,13 @@ int32_t main(int32_t argc, char** argv) {</td>
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9870
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9870
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<pre style="margin: 0;"> <span id="LC9870" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance square</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or plain --distance instead.</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="9871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9871
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<td class="diff-line-num new_line" data-linenumber="9871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9871
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<pre style="margin: 0;"> <span id="LC9871" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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9872
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<td class="diff-line-num new_line" data-linenumber="9872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9872
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<pre style="margin: 0;"> <span id="LC9872" class="line" lang="c"> <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;">dist_calc_type</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">DISTANCE_BIN</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">DISTANCE_BIN4</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;">dist_calc_type</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">DISTANCE_SHAPEMASK</span><span class="p">)))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9873
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<td class="diff-line-num new_line old" data-linenumber="9873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9873" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with plain </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance bin<span class="idiff left right">{,4}</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use e.g.</span><span class="se" style="color: #d14;">\n\"</span><span class="s" style="color: #d14;">--distance bin square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance bin triangle</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead.</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="9873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9873
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<pre style="margin: 0;">+<span id="LC9873" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with plain </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance bin<span class="idiff left right">[4]</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use e.g.</span><span class="se" style="color: #d14;">\n\"</span><span class="s" style="color: #d14;">--distance bin square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--distance bin triangle</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead.</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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9874
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<td class="diff-line-num new_line" data-linenumber="9874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9874
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<pre style="margin: 0;"> <span id="LC9874" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9875
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<td class="diff-line-num new_line" data-linenumber="9875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9875
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<pre style="margin: 0;"> <span id="LC9875" class="line" lang="c"> <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;">rel_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">REL_CALC_SHAPEMASK</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">REL_CALC_SQ</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9876
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<td class="diff-line-num new_line" data-linenumber="9876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9876
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<pre style="margin: 0;"> <span id="LC9876" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel square</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or plain --make-rel instead.</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="9877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9877
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<td class="diff-line-num new_line" data-linenumber="9877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9877
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<pre style="margin: 0;"> <span id="LC9877" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9878
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<td class="diff-line-num new_line" data-linenumber="9878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9878
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<pre style="margin: 0;"> <span id="LC9878" class="line" lang="c"> <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;">rel_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">REL_CALC_BIN</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">REL_CALC_BIN4</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;">rel_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">REL_CALC_SHAPEMASK</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">REL_CALC_GRM_BIN</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9879
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<td class="diff-line-num new_line old" data-linenumber="9879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9879" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with plain </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel bin<span class="idiff left right">{,4}</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use e.g.</span><span class="se" style="color: #d14;">\n\"</span><span class="s" style="color: #d14;">--make-rel bin square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel bin triangle</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9880" style="width: 35px; color: rgba(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="9879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9879
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<pre style="margin: 0;">+<span id="LC9879" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel cannot be used with plain </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel bin<span class="idiff left right">[4]</span></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Use e.g.</span><span class="se" style="color: #d14;">\n\"</span><span class="s" style="color: #d14;">--make-rel bin square0</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--make-rel bin triangle</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead.</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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9880
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<td class="diff-line-num new_line" data-linenumber="9880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9880
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<pre style="margin: 0;"> <span id="LC9880" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9881
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<td class="diff-line-num new_line" data-linenumber="9881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9881
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<pre style="margin: 0;"> <span id="LC9881" class="line" lang="c"> <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;">calculation_type</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CALC_PLINK1_DISTANCE_MATRIX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9882
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<td class="diff-line-num new_line" data-linenumber="9882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9882
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9882" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --parallel and --distance-matrix cannot be used together. Use</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">--distance instead.</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 unfold js-unfold old_line" data-linenumber="10828" style="width: 35px; color: rgba(0,0,0,0.3); 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="10828" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10828,7 +10828,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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10828
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<td class="diff-line-num new_line" data-linenumber="10828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10828
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<pre style="margin: 0;"> <span id="LC10828" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting --r/--r2 modifiers.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10829
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<td class="diff-line-num new_line" data-linenumber="10829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10829
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<pre style="margin: 0;"> <span id="LC10829" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="10830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10830
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<td class="diff-line-num new_line" data-linenumber="10830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10830
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<pre style="margin: 0;"> <span id="LC10830" class="line" lang="c"> <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;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">LD_MATRIX_SPACES</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="10831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10831
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<td class="diff-line-num new_line old" data-linenumber="10831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10831" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">{,4}</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10832" style="width: 35px; color: rgba(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="10831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10831
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<pre style="margin: 0;">+<span id="LC10831" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">[4]</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10832
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<td class="diff-line-num new_line" data-linenumber="10832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10832
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<pre style="margin: 0;"> <span id="LC10832" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10833
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<td class="diff-line-num new_line" data-linenumber="10833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10833
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<pre style="margin: 0;"> <span id="LC10833" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10834
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<td class="diff-line-num new_line" data-linenumber="10834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10834
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<pre style="margin: 0;"> <span id="LC10834" class="line" lang="c"> <span class="n" style="color: #333;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">LD_MATRIX_BIN</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10839" style="width: 35px; color: rgba(0,0,0,0.3); 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="10839" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10839,7 +10839,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10839
</td>
<td class="diff-line-num new_line" data-linenumber="10839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10839
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10839" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Conflicting --r/--r2 modifiers.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10840
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<td class="diff-line-num new_line" data-linenumber="10840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10840
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<pre style="margin: 0;"> <span id="LC10840" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10841
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<td class="diff-line-num new_line" data-linenumber="10841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10841
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<pre style="margin: 0;"> <span id="LC10841" class="line" lang="c"> <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;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">LD_MATRIX_SPACES</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="10842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10842
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<td class="diff-line-num new_line old" data-linenumber="10842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC10842" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">{,4}</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10843" style="width: 35px; color: rgba(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="10842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10842
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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="LC10842" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">[4]</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10843
</td>
<td class="diff-line-num new_line" data-linenumber="10843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10843
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10843" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10844
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<td class="diff-line-num new_line" data-linenumber="10844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10844
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10844" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10845
</td>
<td class="diff-line-num new_line" data-linenumber="10845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10845
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<pre style="margin: 0;"> <span id="LC10845" class="line" lang="c"> <span class="n" style="color: #333;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">LD_MATRIX_BIN4</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10850" style="width: 35px; color: rgba(0,0,0,0.3); 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="10850" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10850,7 +10850,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10850
</td>
<td class="diff-line-num new_line" data-linenumber="10850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10850
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10850" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">LD_INTER_CHR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">LD_INPHASE</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">LD_DX</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">LD_WITH_FREQS</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10851
</td>
<td class="diff-line-num new_line" data-linenumber="10851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10851
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10851" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_r2_matrix_conflict</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10852
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10852
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<pre style="margin: 0;"> <span id="LC10852" class="line" lang="c"> <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;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">LD_MATRIX_BIN</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">LD_MATRIX_BIN4</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="10853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10853
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<td class="diff-line-num new_line old" data-linenumber="10853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10853" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">{,4}</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="10854" style="width: 35px; color: rgba(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="10853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10853
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<pre style="margin: 0;">+<span id="LC10853" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --r/--r2 'bin<span class="idiff left right">[4]</span>' and 'spaces' modifiers cannot be used together.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10854
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<td class="diff-line-num new_line" data-linenumber="10854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10854
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<pre style="margin: 0;"> <span id="LC10854" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="10855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10855
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<td class="diff-line-num new_line" data-linenumber="10855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10855
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<pre style="margin: 0;"> <span id="LC10855" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="10856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10856
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<td class="diff-line-num new_line" data-linenumber="10856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10856
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<pre style="margin: 0;"> <span id="LC10856" class="line" lang="c"> <span class="n" style="color: #333;">ld_info</span><span class="p">.</span><span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">LD_MATRIX_SPACES</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10974" style="width: 35px; color: rgba(0,0,0,0.3); 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="10974" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -10974,7 +10974,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="10974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10974
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<td class="diff-line-num new_line" data-linenumber="10974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10974
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<pre style="margin: 0;"> <span id="LC10974" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --snp cannot be used with --from-bp/-kb/-mb.</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="10975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10975
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<td class="diff-line-num new_line" data-linenumber="10975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10975
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<pre style="margin: 0;"> <span id="LC10975" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="10976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10976
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<td class="diff-line-num new_line" data-linenumber="10976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10976
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<pre style="margin: 0;"> <span id="LC10976" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">are_all_words_zero</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">CHROM_MASK_INITIAL_WORDS</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">incl_excl_name_stack</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="10977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10977
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<td class="diff-line-num new_line old" data-linenumber="10977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10977" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --snp cannot be used with --autosome<span class="idiff left right">{,-xy} or --{,not-}</span>chr.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10978" style="width: 35px; color: rgba(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="10977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10977
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<pre style="margin: 0;">+<span id="LC10977" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --snp cannot be used with --autosome<span class="idiff left right">[-xy] or --[not-]</span>chr.</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="10978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10978
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<td class="diff-line-num new_line" data-linenumber="10978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10978
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<pre style="margin: 0;"> <span id="LC10978" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10979
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<td class="diff-line-num new_line" data-linenumber="10979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10979
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<pre style="margin: 0;"> <span id="LC10979" class="line" lang="c"> <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;">markername_snp</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10980
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<td class="diff-line-num new_line" data-linenumber="10980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10980
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<pre style="margin: 0;"> <span id="LC10980" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --snp cannot be used with --exclude-snp.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11704" style="width: 35px; color: rgba(0,0,0,0.3); 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="11704" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -11704,7 +11704,7 @@ int32_t main(int32_t argc, char** argv) {</td>
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<td class="diff-line-num old_line" data-linenumber="11704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11704
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<td class="diff-line-num new_line" data-linenumber="11704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11704
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11704" class="line" lang="c"> <span class="n" style="color: #333;">load_rare</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">LOAD_RARE_TPED</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="11705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11705
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<td class="diff-line-num new_line" data-linenumber="11705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11705
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<pre style="margin: 0;"> <span id="LC11705" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">memcmp</span><span class="p">(</span><span class="n" style="color: #333;">argptr2</span><span class="p">,</span> <span class="s" style="color: #d14;">"o"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11706
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<td class="diff-line-num new_line" data-linenumber="11706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11706
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<pre style="margin: 0;"> <span id="LC11706" 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;">are_all_words_zero</span><span class="p">(</span><span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">chrom_mask</span><span class="p">,</span> <span class="n" style="color: #333;">CHROM_MASK_INITIAL_WORDS</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">chrom_info</span><span class="p">.</span><span class="n" style="color: #333;">incl_excl_name_stack</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="11707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11707
</td>
<td class="diff-line-num new_line old" data-linenumber="11707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11707" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --to cannot be used with --autosome<span class="idiff left right">{,-xy} or --{,not-}</span>chr.</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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11707
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<pre style="margin: 0;">+<span id="LC11707" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --to cannot be used with --autosome<span class="idiff left right">[-xy] or --[not-]</span>chr.</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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11708
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11708
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<pre style="margin: 0;"> <span id="LC11708" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">main_ret_INVALID_CMDLINE_A</span><span class="p">;</span></span>
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11709
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11709
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<pre style="margin: 0;"> <span id="LC11709" class="line" lang="c"> <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;">markername_snp</span><span class="p">)</span> <span class="p">{</span></span>
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11710
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11710
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<pre style="margin: 0;"> <span id="LC11710" class="line" lang="c"> <span class="n" style="color: #333;">logerrprint</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --to cannot be used with --snp.</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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<a href="https://salsa.debian.org/med-team/plink1-9/commit/152a5d351c04e300680727ddc3ff5e1b5c2d946a#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">@@ -14221,7 +14221,7 @@ int32_t recode(uint32_t recode_modifier, FILE* bedfile, uintptr_t bed_offset, ch</td>
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14221
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14221
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<pre style="margin: 0;"> <span id="LC14221" class="line" lang="c"> <span class="p">}</span></span>
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14222
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14222
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<pre style="margin: 0;"> <span id="LC14222" class="line" lang="c"></span>
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14223
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14223
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<pre style="margin: 0;"> <span id="LC14223" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix: stop generating a .map file when Oxford-format requested</span></span>
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<td class="diff-line-num old old_line" data-linenumber="14224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14224
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<pre style="margin: 0;">-<span id="LC14224" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recode_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">RECODE_COMPOUND</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_LGEN</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_LGEN_REF</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_PED</span><span class="p">))</span> <span class="p">{</span></span>
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14224
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<pre style="margin: 0;">+<span id="LC14224" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recode_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">RECODE_COMPOUND</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_LGEN</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_LGEN_REF</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_PED</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">RECODE_RLIST</span></span><span class="p">))</span> <span class="p">{</span></span>
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14225
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14225
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<pre style="margin: 0;"> <span id="LC14225" class="line" lang="c"> <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;">".map"</span><span class="p">);</span></span>
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14226
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14226
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<pre style="margin: 0;"> <span id="LC14226" 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;">write_map_or_bim</span><span class="p">(</span><span class="n" style="color: #333;">outname</span><span class="p">,</span> <span class="n" style="color: #333;">marker_exclude</span><span class="p">,</span> <span class="n" style="color: #333;">marker_ct</span><span class="p">,</span> <span class="n" style="color: #333;">marker_ids</span><span class="p">,</span> <span class="n" style="color: #333;">max_marker_id_len</span><span class="p">,</span> <span class="n" style="color: #333;">marker_cms</span><span class="p">,</span> <span class="n" style="color: #333;">marker_pos</span><span class="p">,</span> <span class="n" style="color: #333;">nullptr</span><span class="p">,</span> <span class="p">((</span><span class="n" style="color: #333;">recode_modifier</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">RECODE_TAB</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">RECODE_DELIMX</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">RECODE_DELIMX</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_info_ptr</span><span class="p">);</span></span>
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14227
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14227
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<pre style="margin: 0;"> <span id="LC14227" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -833,9 +833,9 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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833
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="c"><span class="s" style="color: #d14;">" * If you're satisfied with all the default settings described below, just</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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834
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="c"><span class="s" style="color: #d14;">" use --homozyg with no modifiers. Otherwise, --homozyg lets you change a</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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835
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="c"><span class="s" style="color: #d14;">" few binary settings:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="c"><span class="s" style="color: #d14;">" * 'group<span class="idiff left right">{,-verbose}</span>' adds a report on pools of overlapping runs of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="c"><span class="s" style="color: #d14;">" * 'group<span class="idiff left right">[-verbose]</span>' adds a report on pools of overlapping runs of</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="LC837" class="line" lang="c"><span class="s" style="color: #d14;">" homozygosity. (Automatically set when --homozyg-match is present.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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838
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="c"><span class="s" style="color: #d14;">" * With 'group<span class="idiff left right">{,-verbose}</span>', 'consensus-match' causes pairwise segmental</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="LC838" class="line" lang="c"><span class="s" style="color: #d14;">" * With 'group<span class="idiff left right">[-verbose]</span>', 'consensus-match' causes pairwise segmental</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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839
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="c"><span class="s" style="color: #d14;">" matches to be called based on the variants in the pool's consensus</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="c"><span class="s" style="color: #d14;">" segment, rather than the variants in the pairwise intersection.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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841
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="c"><span class="s" style="color: #d14;">" * Due to how the scanning window algorithm works, it is possible for a</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">@@ -1253,7 +1253,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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1253
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1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="c"><span class="s" style="color: #d14;">" * 'nop' strips p-values from the main report.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1254
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1254
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="c"><span class="s" style="color: #d14;">" * These computations can be subdivided with --parallel; however...</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="LC1255" class="line" lang="c"><span class="s" style="color: #d14;">" --epistasis-summary-merge <common file prefix> <ct></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="LC1256" class="line" lang="c"><span class="s" style="color: #d14;">" When a --<span class="idiff left right">{,fast-}</span>epistasis job is subdivided with --parallel, the main</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="LC1256" class="line" lang="c"><span class="s" style="color: #d14;">" When a --<span class="idiff left right">[fast-]</span>epistasis job is subdivided with --parallel, the main</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="LC1257" class="line" lang="c"><span class="s" style="color: #d14;">" report can be assembled at the end by applying Unix 'cat' in the usual</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="LC1258" class="line" lang="c"><span class="s" style="color: #d14;">" manner, but the .summary.1, .summary.2, ... files may require a specialized</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="LC1259" class="line" lang="c"><span class="s" style="color: #d14;">" merge. --epistasis-summary-merge takes care of the latter.</span><span class="se" style="color: #d14;">\n\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">@@ -1407,8 +1407,8 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="c"><span class="s" style="color: #d14;">" --simulate-n <num> : Set --simulate-qt sample count (default 1000).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="c"> <span class="p">);</span></span>
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"simulate</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">simulate-qt</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">simulate-label</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">simulate-missing"</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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1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="c"><span class="s" style="color: #d14;">" --simulate-label <prefix> : Set --simulate<span class="idiff left right">{,-qt}</span> FID/IID name prefix.</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="LC1411" class="line" lang="c"><span class="s" style="color: #d14;">" --simulate-missing <freq> : Set --simulate<span class="idiff left right">{,-qt}</span> missing genotype frequency.</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="LC1410" class="line" lang="c"><span class="s" style="color: #d14;">" --simulate-label <prefix> : Set --simulate<span class="idiff left right">[-qt]</span> FID/IID name prefix.</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="LC1411" class="line" lang="c"><span class="s" style="color: #d14;">" --simulate-missing <freq> : Set --simulate<span class="idiff left right">[-qt]</span> missing genotype frequency.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> <span class="p">);</span></span>
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1413
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1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"allow-extra-chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">aec"</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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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="c"><span class="s" style="color: #d14;">" --allow-extra-chr ['0'] : Permit unrecognized chromosome codes. The '0'</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">@@ -1638,7 +1638,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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1638
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="c"> <span class="p">);</span></span>
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1639
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<td class="diff-line-num new_line" data-linenumber="1639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"read-freq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">update-freq"</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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1640
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1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="c"><span class="s" style="color: #d14;">" --read-freq <fn> : Estimate MAFs and heterozygote frequencies from the given</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1641
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<pre style="margin: 0;">-<span id="LC1641" class="line" lang="c"><span class="s" style="color: #d14;">" --freq<span class="idiff left right">{,x}</span> report, instead of the input fileset.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1641
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="c"><span class="s" style="color: #d14;">" --freq<span class="idiff left right">[x]</span> report, instead of the input fileset.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1642
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1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="c"> <span class="p">);</span></span>
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1643
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"hwe</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">hwe-all</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">hwe2"</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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1644
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"><span class="s" style="color: #d14;">" --hwe <p> ['midp'] ['include-nonctrl'] : Exclude variants with Hardy-Weinberg</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">@@ -1813,7 +1813,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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1813
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<pre style="margin: 0;"> <span id="LC1813" class="line" lang="c"><span class="s" style="color: #d14;">" covariate file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1814
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1814
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<pre style="margin: 0;"> <span id="LC1814" class="line" lang="c"> <span class="p">);</span></span>
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1815
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"merge</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bmerge</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">merge-list</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">merge-mode"</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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1816
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<pre style="margin: 0;">-<span id="LC1816" class="line" lang="c"><span class="s" style="color: #d14;">" --merge-mode <n> : Adjust --<span class="idiff left right">{,b}</span>merge/--merge-list behavior based on a</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1816
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<pre style="margin: 0;">+<span id="LC1816" class="line" lang="c"><span class="s" style="color: #d14;">" --merge-mode <n> : Adjust --<span class="idiff left right">[b]</span>merge/--merge-list behavior based on a</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1817
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1817
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="c"><span class="s" style="color: #d14;">" numeric code.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1818
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1818
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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="c"><span class="s" style="color: #d14;">" 1 (default) = ignore missing calls, otherwise difference</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="LC1819" class="line" lang="c"><span class="s" style="color: #d14;">" -> missing</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">@@ -1853,7 +1853,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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1853
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1853
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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="c"><span class="s" style="color: #d14;">" --tag-mode2 : Use two-column --show-tags (file mode) I/O format.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1854
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1854
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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="c"> <span class="p">);</span></span>
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1855
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1855
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<pre style="margin: 0;"> <span id="LC1855" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"indep</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">indep-pairwise</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">r</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">r2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">flip-scan</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">flipscan</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">show-tags</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ld-xchr"</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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1856
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<pre style="margin: 0;">-<span id="LC1856" class="line" lang="c"><span class="s" style="color: #d14;">" --ld-xchr <code> : Set chrX model for --indep<span class="idiff left right">{,-pairwise}</span>, --r/--r2,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="c"><span class="s" style="color: #d14;">" --ld-xchr <code> : Set chrX model for --indep<span class="idiff left right">[-pairwise]</span>, --r/--r2,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1857
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1857
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<pre style="margin: 0;"> <span id="LC1857" class="line" lang="c"><span class="s" style="color: #d14;">" --flip-scan, and --show-tags.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1858
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1858
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<pre style="margin: 0;"> <span id="LC1858" class="line" lang="c"><span class="s" style="color: #d14;">" 1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1859
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="c"><span class="s" style="color: #d14;">" 2 = males coded 0/2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2090" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2090,7 +2090,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {</td>
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2090
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2090
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<pre style="margin: 0;"> <span id="LC2090" class="line" lang="c"> <span class="p">);</span></span>
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2091
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2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="c"> <span class="n" style="color: #333;">help_print</span><span class="p">(</span><span class="s" style="color: #d14;">"fast-epistasis</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">epistasis</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gap</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">epi1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">epi2"</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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2092
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2092
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="c"><span class="s" style="color: #d14;">" --gap <kbs> : Set </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">--fast-epistasis case-only</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> min. gap (default 1000).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2093
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<pre style="margin: 0;">-<span id="LC2093" class="line" lang="c"><span class="s" style="color: #d14;">" --epi1 <p-value> : Set --<span class="idiff left right">{,fast-}</span>epistasis reporting threshold (default</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="c"><span class="s" style="color: #d14;">" --epi1 <p-value> : Set --<span class="idiff left right">[fast-]</span>epistasis reporting threshold (default</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2094
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2094
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<pre style="margin: 0;"> <span id="LC2094" class="line" lang="c"><span class="s" style="color: #d14;">" 5e-6 for 'boost', 1e-4 otherwise).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2095
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2095
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="c"><span class="s" style="color: #d14;">" --epi2 <p-value> : Set threshold for contributing to SIG_E count (def. 0.01).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2096
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2096
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="c"> <span class="p">);</span></span>
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