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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/ad995bf0cc031cd9ceac079a229c6f8d61d4328d">ad995bf0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-19T10:07:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/efc421d80f2b32c66f09d73c84b3232fcd9b6000">efc421d8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-19T10:07:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.33+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/49ec6958a63b5db29cb30511227ef1f089a34bc8">49ec6958</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-19T10:07:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.5.33+dfsg'
Update to upstream version '2.5.33+dfsg'
with Debian dir 7c83d9a0c52cd6359f0665da985fcbe33476d838</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/70e886272ce6e5a8128c0f4acfcc5d22b3594cee">70e88627</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-19T10:07:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/723d9eb927a404b4fb43e0a48a6e0ed5adec28c3">723d9eb9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-19T10:07:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>8 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#817efc81f1180519a6136b50a447433f20cf679d">
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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<li class="file-stats">
<a href="#428ab1297972e0944fd35b5136d40326dd840dcb">
res/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
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<li class="file-stats">
<a href="#65ee9d47988109d0925fe3692b68b7b246e7fc1d">
res/TemplateBatchFiles/libv3/IOFunctions.bf
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<li class="file-stats">
<a href="#5dfec713e3892a936e8b5a63db56c03bee3ec252">
res/TemplateBatchFiles/libv3/all-terms.bf
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<li class="file-stats">
<a href="#e7b72a8f9f424fe1e9e9e76f25522816189c14c9">
res/TemplateBatchFiles/libv3/tasks/alignments.bf
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># paste config here</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">slack</span><span class="pi">:</span> <span class="s" style="color: #d14;">veg-igem:rqQd95zjTuZoRNElekQx2CLf</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">recipients</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">steven@stevenweaver.org</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">spond@temple.edu</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_success</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">only</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">develop</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export OMP_NUM_THREADS=4</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">travis_wait 60 eval $envSpecificTest</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-9</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-9</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-9" CC="gcc-9"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="export PATH=$PATH:$(pwd); cd; git clone https://gitlab.com/rdvelazquez/testiphy.git; cd testiphy; ./testiphy HYPHYMP"</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="make test"</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-9</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-9</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-9" CC="gcc-9"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># ---- Just run the hbl unit tests with gcc-4, 5 and 6 ----</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># gcc-4</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="bash ./run_unit_tests.sh"</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.9</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-4.9</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-4.9" CC="gcc-4.9"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># gcc-5</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="bash ./run_unit_tests.sh"</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-5</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-5</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="yaml"></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># gcc-6</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="bash ./run_unit_tests.sh"</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-6</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-6</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># gcc-7</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="bash ./run_unit_tests.sh"</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-7</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-7</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># gcc-8</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">envSpecificTest="bash ./run_unit_tests.sh"</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">llvm-toolchain-precise</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">george-edison55-precise-backports</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-8</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc-8</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ "$CXX" = "g++" ]; then export CXX="g++-8" CC="gcc-8"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake .</span> </span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.33+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Tue, 19 Oct 2021 10:07:52 +0000</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">hyphy (2.5.32+dfsg-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version 2.5.32+dfsg</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libsqlite3-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> chrpath</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/hyphy</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/hyphy.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://hyphy.org/</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#817efc81f1180519a6136b50a447433f20cf679d"><strong>res/TemplateBatchFiles/SelectionAnalyses/FEL.bf</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">@@ -134,7 +134,7 @@ if (^"fel.ci") {</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Synonymous substitution rate at a site"}</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous substitution rate at a site"}</span></span>
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136
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha=beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The rate estimate under the neutral model"}</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ratio<span class="idiff left right">n</span> test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ratio test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Asymptotic p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for evidence of selection</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> beta &neq; alpha"}</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Total branch length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS"}</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"dN/dS LB"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "95% profile likelihood CI lower bound for dN/dS (if available)"}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(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">@@ -148,7 +148,7 @@ if (^"fel.ci") {</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers = {{"alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Synonymous substitution rate at a site"}</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous substitution rate at a site"}</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"alpha=beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The rate estimate under the neutral model"}</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ratio<span class="idiff left right">n</span> test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Likelihood ratio test statistic for beta = alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> versus beta &neq; alpha"}</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Asymptotic p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for evidence of selection</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> beta &neq; alpha"}</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {"Total branch length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS"}};</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_screen_output = {{"Codon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Partition"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Selection detected?"}};</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">@@ -406,7 +406,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" = 1;</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_nuisance" = 1;</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -417,24 +416,27 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = None;</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci") {</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv") {</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lf_stash = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">TakeLFStateSnapshot (lf);</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global omega_ratio_for_ci;</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" == 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0) { // has no syn_variation</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" = 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">8;</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 10000;</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0;</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci = ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" / ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (!sim_mode) {</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv") {</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lf_stash = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">TakeLFStateSnapshot (lf);</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> global omega_ratio_for_ci;</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" == 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0) { // has no syn_variation</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler" = 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">8;</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 10000;</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci :</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0;</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> omega_ratio_for_ci = ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" / ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" := omega_ratio_for_ci * ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI (&omega_ratio_for_ci</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_stash);</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test" := omega_ratio_for_ci * ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha_scaler";</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI (&omega_ratio_for_ci</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf_stash);</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta_scaler_test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ci = None;</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (sim_mode) {</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">@@ -456,8 +458,10 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Null </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (!sim_mode) {</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> tree_name = (lfInfo</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Trees"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sum = (BranchLength (^tree_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1)*^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches_index")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample") {</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> N = ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample";</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sims = {};</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">@@ -474,12 +478,14 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> is = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">handle_a_site (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> sims</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> pattern_info</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> null_LRT</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = is;</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative") : alternative</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null"): Null</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"): null_LRT};</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative") : alternative</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null"): Null</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"): null_LRT</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> utility</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">getGlobalValue("terms</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">confidence_interval"): ci</span>};</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative") : alternative</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null"): Null</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sum") : sum</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"): ci};</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="brainfuck"></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">@@ -581,18 +587,21 @@ lfunction fel.store_results (node, result, arguments) {</td>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } };</span></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> has_lrt = FALSE;</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != result) { // not a constant site</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt = math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DoLRT ((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (result / ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated") {</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> has_lrt = result / ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated";</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (has_lrt) {</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pv = </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"_MATRIX_ELEMENT_VALUE_</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">=" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT")</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (pv</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)/(1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample");</span></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } </span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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596
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha");</span></span>
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta");</span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta");</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">@@ -600,17 +609,19 @@ lfunction fel.store_results (node, result, arguments) {</td>
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = lrt </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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601
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="brainfuck"></span>
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right">sum = 0;</span></span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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604
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*alternative_lengths = ((result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> tname = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test");</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_; in; ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names") {</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_class_ = ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_node_class_ == tname) {</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> sum </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= ((alternative_lengths)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '_node_class_ = ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">`&partition_index`</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_node_class_ == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `&sum` </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= ((`&alternative_lengths`)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');*/</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sum;</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sum"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (None != result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lower_bound"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -621,13 +632,18 @@ lfunction fel.store_results (node, result, arguments) {</td>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="brainfuck"></span>
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index);</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (has_lrt) {</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_LRT"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index);</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_fel_result_; in; pattern_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_fel_result_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result_row;</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">echo (_fel_result_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> result_row);</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (has_lrt) {</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_LRT")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_fel_result_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (pattern_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_fel_result_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">`&partition_index`</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_fel_result_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = `&result_row`;</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">echo (_fel_result_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> `&partition_index`</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> `&result_row`);</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //assert (0);</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">@@ -635,6 +651,7 @@ lfunction fel.store_results (node, result, arguments) {</td>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//</span><span class="nf" style="color: #900; font-weight: 600;">----------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results = {};</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_LRT = {};</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index = 0; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_count; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header_done = FALSE;</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">@@ -650,17 +667,22 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> // beta = beta_scaler_test * branch_length or beta_nuisance_test * branch_length</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> SetParameter (DEFER_CONSTRAINT_APPLICATION</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0);</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches_index = {1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names)</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1};</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i = 0;</span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_; in; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names) {</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_class_ = (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_node_class_ == terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test) {</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches_index </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scalers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scalers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scalers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> (( fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '_node_class_ = (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="695" style="width: 35px; color: rgba(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="717" style="width: 35px; color: rgba(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">@@ -695,7 +717,7 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue = mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CreateQueue ({"LikelihoodFunctions": {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Models" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mg_rev"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Headers" : {{"libv3/all</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"libv3/tasks/alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Variables" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci"}}</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Variables" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci"</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">"fel</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">selected_branches_index"</span>}}</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> });</span></span>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="brainfuck"></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">@@ -735,32 +757,35 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par</td>
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ClearProgressBar();</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueComplete (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue);</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix = {Abs (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Rows (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers)};</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_key_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_key_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _value_; in; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index = 0; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> Rows (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers); fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">_key_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="brainfuck"></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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748
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix;</span></span>
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="brainfuck"></span>
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="brainfuck"></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE </span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">headers : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">content : fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results };</span></span>
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample) {</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE </span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_LRT;</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="brainfuck"></span>
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("fel"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "** Found _" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">counts</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "_ sites under pervasive positive diversifying and _" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">counts</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "_ sites under negative selection at p </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pvalue </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "**");</span></span>
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="brainfuck"></span>
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759
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Total time");</span></span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stopTimer (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "FEL analysis");</span></span>
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resamples) {</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resamples;</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample) {</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">simulated</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">resample;</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="brainfuck"></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ci) {</span></span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">confidence_interval</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = TRUE;</span></span>
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="brainfuck"></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">GetString (_hpv</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">HYPHY_VERSION</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0);</span></span>
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<li id="428ab1297972e0944fd35b5136d40326dd840dcb">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#428ab1297972e0944fd35b5136d40326dd840dcb"><strong>res/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(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">@@ -139,7 +139,6 @@ selection.io.startTimer (fubar.json [terms.json.timers], "Overall", 0);</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">base = (fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">input</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="brainfuck"></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("cache"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Save FUBAR cache to </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">default is alignment</span><span class="nf" style="color: #900; font-weight: 600;">+.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">base </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache");</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("output"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Save FUBAR results (JSON) to </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">default is alignment</span><span class="nf" style="color: #900; font-weight: 600;">+.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json");</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*</span><span class="nf" style="color: #900; font-weight: 600;">------------------------------------------------------------------------------</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">@@ -149,6 +148,9 @@ KeywordArgument ("output", "Save FUBAR results (JSON) to [default is alignment</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForString ("Save FUBAR cache to");</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCacheFromFile (fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache);</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("output"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Save FUBAR results (JSON) to </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">default is alignment</span><span class="nf" style="color: #900; font-weight: 600;">+.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json");</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save the resulting JSON file to");</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options = {terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header : TRUE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">minimum_column_width: 16</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">align : "center"};</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ( "</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> FUBAR will write cache and result files to _`fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">base`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cache_ and _`fubar</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">path</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">base`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FUBAR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> respectively \n\n");</span></span>
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<li id="65ee9d47988109d0925fe3692b68b7b246e7fc1d">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#65ee9d47988109d0925fe3692b68b7b246e7fc1d"><strong>res/TemplateBatchFiles/libv3/IOFunctions.bf</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">@@ -148,7 +148,7 @@ lfunction io.SpoolJSON(json, file) {</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param file</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ParseJSON(file_path) {</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fscanf(file_path</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Raw"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> test);</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fscanf(file_path</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left">REWIND</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"> </span>"Raw"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> test);</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parsed_test = Eval(test);</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return parsed_test;</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#5dfec713e3892a936e8b5a63db56c03bee3ec252"><strong>res/TemplateBatchFiles/libv3/all-terms.bf</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">@@ -30,6 +30,7 @@ namespace terms{</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> data_type = "datatype";</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> devnull = "/dev/null";</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _namespace = "namespace";</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> warning = "warning";</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> category = "category";</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> mixture = "mixture";</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3#e7b72a8f9f424fe1e9e9e76f25522816189c14c9"><strong>res/TemplateBatchFiles/libv3/tasks/alignments.bf</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">@@ -335,6 +335,17 @@ function alignments.PromptForGeneticCodeAndAlignment(dataset_name, datafilter_na</td>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile(dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> datafilter_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReadCodonDataSet(dataset_name));</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Prompts user for genetic code and alignment; do not create error condition on stop codons</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptForGeneticCodeAndAlignmentWarnStops</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} dataset_name </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the name of the dataset you wish to use</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} datafilter_name </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the name of the dataset filter you wish to use</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @returns {Dictionary} r </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> metadata pertaining to the dataset</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptForGeneticCodeAndAlignmentWarnStops (dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> datafilter_name) {</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFileWarnStops(dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> datafilter_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReadCodonDataSet(dataset_name));</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Loads genetic code and alignment from file path</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadGeneticCodeAndAlignment</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">@@ -393,6 +404,51 @@ function alignments.LoadCodonDataFile(dataset_name, datafilter_name, data_info)</td>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return data_info;</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Creates codon dataset filter from data set; do not treat stop codons as an error condition</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFileWarnStops</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} datafilter_name </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the name of the dataset filter you wish to use</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} dataset_name </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the name of the existing dataset</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Dictionary} data_info </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> DataSet metadata information</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @returns {Dictionary} updated data_info that includes the number of sites</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> dataset</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and datafilter name</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFileWarnStops(dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> datafilter_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> data_info) {</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter ^ datafilter_name = CreateFilter( ^ dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 3</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stop_codons</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"`datafilter_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites"*3 != ^"`dataset_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites") {</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> // generate a more diagnostic error here</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">warning"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i = 0; alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> ^"`dataset_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">species"; alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter ^datafilter_name = CreateFilter( ^ dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 3</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stop_codons</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"`datafilter_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites"*3 != ^"`dataset_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites") {</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">name = alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetIthSequenceOriginalName (dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i);</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_map = ^"`datafilter_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_map";</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">annotation_string = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PopulateDict (0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"`dataset_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '(alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">name</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sequence</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_idx</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">'</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '_idx');</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_map</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `&alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">annotation_string`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_value_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = `&alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">annotation_string`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_value_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> && 0;</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">warning"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">name</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">id</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = Join (""</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadCodonDataFile</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">annotation_string);</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter ^ datafilter_name = CreateFilter( ^ dataset_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 3</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">stop_codons</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^ "`datafilter_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites";</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">dataset</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = dataset_name;</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">datafilter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = datafilter_name;</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return data_info;</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Creates nucleotide dataset filter from file</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReadNucleotideAlignment</span></span>
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