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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/521762b6496a66f06cfecb78475f287f13fe7577">521762b6</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-08-22T16:11:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.4-180807</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
plink.c
</a>
</li>
<li class="file-stats">
<a href="#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69">
plink_assoc.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
<a href="https://salsa.debian.org/med-team/plink1-9/commit/521762b6496a66f06cfecb78475f287f13fe7577#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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<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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<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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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90b6.<span class="idiff left right">3</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.<span class="idiff left right">4</span>"</span></span>
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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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98
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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 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">@@ -105,10 +105,10 @@ static const char ver_str[] =</td>
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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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<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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<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">17 Jul</span> 2018)"</span><span class="p">;</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">7 Aug</span> 2018)"</span><span class="p">;</span></span>
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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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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">""</span></span>
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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 class="idiff left right"> </span>"</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="s" style="color: #d14;">" "</span> <span class="c1" style="color: #998; font-style: italic;">// (don't want this when version number has two trailing digits)</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<li id="60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69">
<a href="https://salsa.debian.org/med-team/plink1-9/commit/521762b6496a66f06cfecb78475f287f13fe7577#60ba2e8c9bebd9c7595f0590d0e02b4dac6e4a69"><strong>plink_assoc.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5918" style="width: 35px; color: rgba(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="5918" style="width: 35px; color: rgba(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">@@ -5918,6 +5918,8 @@ int32_t model_assoc_set_test(pthread_t* threads, FILE* bedfile, uintptr_t bed_of</td>
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<pre style="margin: 0;"> <span id="LC5918" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC5919" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">model_assoc_set_test_perms_done</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="5920" style="width: 35px; color: rgba(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="LC5920" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC5921" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (7 Aug 2018): forgot to update marker_unstopped_ct</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5922" class="line" lang="c"> <span class="n" style="color: #333;">marker_unstopped_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">popcount_longs</span><span class="p">(</span><span class="n" style="color: #333;">unstopped_markers</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">marker_ct</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BITCT</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">BITCT</span><span class="p">);</span></span>
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<td class="diff-line-num new_line" data-linenumber="5923" style="width: 35px; color: rgba(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="LC5923" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new_line" data-linenumber="5924" style="width: 35px; color: rgba(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="LC5924" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">%u permutation%s complete."</span><span class="p">,</span> <span class="n" style="color: #333;">perms_done</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">perms_done</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"s"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="diff-line-num new_line" data-linenumber="5925" style="width: 35px; color: rgba(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="LC5925" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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