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<h3>

Nilesh Patra pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285">d19d29e5</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-23T22:21:53+05:30</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 12.0.0</pre>

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<h4>8 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

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<li class="file-stats">

<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">

augur/__version__.py

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<li class="file-stats">

<a href="#a34bf74715b32df68fd126394c3bf543847de1da">

augur/distance.py

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<li class="file-stats">

<a href="#1058ed03848375e3c1a8b82623654cb578984455">

augur/filter.py

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<li class="file-stats">

<a href="#104ddc27c2db78b040d33b5412a2de3d66f15177">

augur/refine.py

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<li class="file-stats">

<a href="#5aa84eddf9e5286c15160859a367e2b67129d7d8">

augur/tree.py

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<a href="#0698fd06e0fd6334ba03f49c4d5fcab894112ff2">

tests/functional/filter.t

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<li class="file-stats">

<a href="#f11f72e22ad9db7339f7290c375885f5e6f24b6c">

tests/test_filter.py

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<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</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">@@ -3,6 +3,30 @@</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## __NEXT__</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 12.0.0 (13 April 2021)</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Major Changes</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> filter: Date bounds (<span class="sb" style="color: #d14;">`--min-date`</span> and <span class="sb" style="color: #d14;">`--max-date`</span>) are now inclusive instead of exclusive such that records matching the given dates will pass date filters <span class="p">[</span><span class="nv" style="color: #008080;">#708</span><span class="p">][]</span> (@benjaminotter)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">*</span> refine: Recommend an alternate action when skyline optimization fails <span class="p">[</span><span class="nv" style="color: #008080;">#712</span><span class="p">][]</span> (@huddlej)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">*</span> distance: Count insertion/deletion events once in pairwise distances <span class="p">[</span><span class="nv" style="color: #008080;">#698</span><span class="p">][]</span> (@huddlej, @benjaminotter)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> distance: Optionally ignore specific list of characters defined in a distance map's top-level <span class="sb" style="color: #d14;">`ignored_characters`</span> list <span class="p">[</span><span class="nv" style="color: #008080;">#707</span><span class="p">][]</span> (@benjaminotter)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> filter: Allow <span class="sb" style="color: #d14;">`--subsample-max-sequences`</span> without <span class="sb" style="color: #d14;">`--group-by`</span> <span class="p">[</span><span class="nv" style="color: #008080;">#710</span><span class="p">][]</span> (@benjaminotter)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">*</span> tree: Prefer <span class="sb" style="color: #d14;">`iqtree2`</span> binary over <span class="sb" style="color: #d14;">`iqtree`</span> when possible <span class="p">[</span><span class="nv" style="color: #008080;">#711</span><span class="p">][]</span> (@benjaminotter)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#698</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/698</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#707</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/707</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#708</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/708</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#710</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/710</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#711</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/711</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#712</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/712</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 11.3.0 (19 March 2021)</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

</pre>

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</li>

<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left right">1.3</span>.0'</span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left right">2.0</span>.0'</span></span>

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_augur_version_compatible</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="a34bf74715b32df68fd126394c3bf543847de1da">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#a34bf74715b32df68fd126394c3bf543847de1da"><strong>augur/distance.py</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">@@ -135,6 +135,7 @@ import Bio</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Bio.Phylo</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">distance_map</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_distance_between_nodes</span><span class="p">(</span><span class="n" style="color: #333;">node_a_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">distance_map</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_distance_between_nodes</span><span class="p">(</span><span class="n" style="color: #333;">node_a_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">distance_map</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">aggregate_function</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">max</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">    <span class="s" style="color: #d14;">"""Calculate distance between the two given nodes using the given distance map.</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;">    In cases where the distance map between sequences is asymmetric, the first</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">@@ -245,15 +246,137 @@ def get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 0.0, "map": {"gene": {2: {('T', 'G'): 0.5}}}}</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_b_sequences, node_a_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"><span class="s" style="color: #d14;">    0.0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;">    Treat a single indel as one event.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_a_sequences = {"gene": "ACTG"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_b_sequences = {"gene": "A--G"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 1, "map": {}}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"><span class="s" style="color: #d14;">    1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"><span class="s" style="color: #d14;">    Use the maximum weight of all sites affected by an indel with a site-specific distance map.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 0, "map": {"gene": {1: 1, 2: 2}}}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"><span class="s" style="color: #d14;">    2</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"><span class="s" style="color: #d14;">    Use the maximum weight of all mutations at all sites affected by an indel with a mutation-specific distance map.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "default": 0,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

268

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "map": {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

269

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="s" style="color: #d14;">    ...         "gene": {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

270

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"><span class="s" style="color: #d14;">    ...             1: {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

271

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', 'G'): 1,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

272

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', 'A'): 2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;">    ...             },</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

274

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;">    ...             2: {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', 'G'): 3,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', 'A'): 2</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

277

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;">    ...             }</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

278

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;">    ...         }</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

279

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;">    ...     }</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

280

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;">    ... }</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

282

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;">    3</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

283

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;">    Use the maximum weight of gaps at all sites affected by an indel with a mutation-specific distance map.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "default": 0,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "map": {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;">    ...         "gene": {</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;">    ...             1: {</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', '-'): 1,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', 'A'): 2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;">    ...             },</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;">    ...             2: {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', 'G'): 3,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', '-'): 2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;">    ...             }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"><span class="s" style="color: #d14;">    ...         }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;">    ...     }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"><span class="s" style="color: #d14;">    ... }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;">    2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"><span class="s" style="color: #d14;">    If the default value is greater than any of the site-specific mismatches and</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"><span class="s" style="color: #d14;">    the specific mismatch does not have a weighted defined, use the default</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"><span class="s" style="color: #d14;">    weight.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "default": 4,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;">    ...     "map": {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;">    ...         "gene": {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"><span class="s" style="color: #d14;">    ...             1: {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', 'G'): 1,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('C', 'A'): 2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;">    ...             },</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;">    ...             2: {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', 'G'): 3,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;">    ...                 ('T', 'A'): 2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;">    ...             }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"><span class="s" style="color: #d14;">    ...         }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="s" style="color: #d14;">    ...     }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"><span class="s" style="color: #d14;">    ... }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;">    4</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;">    Count mismatches adjacent to indel events.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_a_sequences = {"gene": "ACTGTA"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_b_sequences = {"gene": "A--CCA"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 1, "map": {}}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;">    3</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"><span class="s" style="color: #d14;">    Ignore specific characters defined in the distance map.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_a_sequences = {"gene": "ACTGG"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;">    >>> node_b_sequences = {"gene": "A--GN"}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 1, "ignored_characters":["-"], "map": {}}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"><span class="s" style="color: #d14;">    1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"><span class="s" style="color: #d14;">    >>> distance_map = {"default": 1, "ignored_characters":["-", "N"], "map": {}}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"><span class="s" style="color: #d14;">    >>> get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"><span class="s" style="color: #d14;">    0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">    <span class="n" style="color: #333;">distance_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">    <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distance_type</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python">    <span class="n" style="color: #333;">ignored_characters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distance_map</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"ignored_characters"</span><span class="p">,[])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">node_a_sequences</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python">        <span class="n" style="color: #333;">gene_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># In a first pass, find all mismatches between the given sequences. Use</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># this pass to identify all sites in insertion/deletion (indel) events,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># so we can calculate an aggregate weight per event. Track each event by</span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># its start site.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python">        <span class="n" style="color: #333;">mismatches_by_site</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python">        <span class="n" style="color: #333;">in_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">gene_length</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]:</span></span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python">                <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ignored_characters</span></span>

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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python">                <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ignored_characters</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">in_gap</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python">                        <span class="n" style="color: #333;">gap_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">site</span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python">                        <span class="n" style="color: #333;">in_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python">                    <span class="n" style="color: #333;">mismatches_by_site</span><span class="p">[</span><span class="n" style="color: #333;">gap_start</span><span class="p">].</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">site</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python">                    <span class="n" style="color: #333;">in_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python">                    <span class="n" style="color: #333;">mismatches_by_site</span><span class="p">[</span><span class="n" style="color: #333;">site</span><span class="p">].</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">site</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python">                <span class="n" style="color: #333;">in_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Sum distances across mismatched sites, aggregating indel events by a</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># summary function (e.g., max, mean, etc.).</span></span>

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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sites</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mismatches_by_site</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python">            <span class="n" style="color: #333;">mismatch_distances</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sites</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">site</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Distances can be provided as either site- and</span></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># sequence-specific dictionaries of sequence pairs to</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -262,14 +385,36 @@ def get_distance_between_nodes(node_a_sequences, node_b_sequences, distance_map)</td>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python">                        <span class="n" style="color: #333;">seq_ancestral</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_a_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">                        <span class="n" style="color: #333;">seq_derived</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_b_sequences</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python">                        <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">].</span><span class="n" style="color: #333;">get</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python">                            <span class="p">(</span><span class="n" style="color: #333;">seq_ancestral</span><span class="p">,</span> <span class="n" style="color: #333;">seq_derived</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python">                            <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">                        <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Check first for a user-defined weight for the</span></span>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># mismatched bases. This supports mismatch weights</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># between specific characters including gaps.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq_ancestral</span><span class="p">,</span> <span class="n" style="color: #333;">seq_derived</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python">                            <span class="n" style="color: #333;">mismatch_distances</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python">                                <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">][(</span><span class="n" style="color: #333;">seq_ancestral</span><span class="p">,</span> <span class="n" style="color: #333;">seq_derived</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Next, check whether the mismatch is a gap. We want to</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># take the aggregate of all weights at this site.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">                        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">seq_ancestral</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">seq_derived</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python">                            <span class="n" style="color: #333;">mismatch_distances</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python">                                <span class="n" style="color: #333;">aggregate_function</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">                                    <span class="n" style="color: #333;">chain</span><span class="p">(</span></span>

</pre>

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402

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python">                                        <span class="p">(</span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">],),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python">                                        <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python">                                    <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python">                                <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Finally, use the default weight, if no</span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># sequence-specific weights are defined.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python">                            <span class="n" style="color: #333;">mismatch_distances</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">distance</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">mismatch_distances</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"map"</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">][</span><span class="n" style="color: #333;">site</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="414" 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="LC272" class="line" lang="python">                    <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python">                    <span class="n" style="color: #333;">mismatch_distances</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">distance_map</span><span class="p">[</span><span class="s" style="color: #d14;">"default"</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Aggregate the distances for all sites in the current mismatch.</span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python">            <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">aggregate_function</span><span class="p">(</span><span class="n" style="color: #333;">mismatch_distances</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">distance_type</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">distance</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>

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</li>

<li id="1058ed03848375e3c1a8b82623654cb578984455">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#1058ed03848375e3c1a8b82623654cb578984455"><strong>augur/filter.py</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">@@ -105,8 +105,8 @@ def register_arguments(parser):</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;">        Uses Pandas Dataframe querying, see https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#indexing-query for syntax.</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;">        (e.g., --query "country == 'Colombia'" or --query "(country == 'USA' & (division == 'Washington'))")"""</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">    <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--min-date'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numeric_date</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimal cutoff for date; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--max-date'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numeric_date</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximal cutoff for date; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--min-date'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numeric_date</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minimal cutoff for date<span class="idiff left right">, the cutoff date is inclusive</span>; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--max-date'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">numeric_date</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"maximal cutoff for date<span class="idiff left right">, the cutoff date is inclusive</span>; may be specified as an Augur-style numeric date (with the year as the integer part) or YYYY-MM-DD"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--exclude-ambiguous-dates-by'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'any'</span><span class="p">,</span> <span class="s" style="color: #d14;">'day'</span><span class="p">,</span> <span class="s" style="color: #d14;">'month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Exclude ambiguous dates by day (e.g., 2020-09-XX), month (e.g., 2020-XX-XX), year (e.g., 200X-10-01), or any date fields. An ambiguous year makes the corresponding month and day ambiguous, too, even if those fields have unambiguous values (e.g., "201X-10-01"). Similarly, an ambiguous month makes the corresponding day ambiguous (e.g., "2010-XX-01").'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">    <span class="n" style="color: #333;">metadata_filter_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--exclude'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file(s) with list of strains to exclude"</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(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">@@ -125,7 +125,7 @@ def register_arguments(parser):</td>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">    <span class="n" style="color: #333;">subsample_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--group-by'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"categories with respect to subsample; two virtual fields, </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">month</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> and </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">year</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">, are supported if they don't already exist as real fields but a </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">date</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> field does exist"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">    <span class="n" style="color: #333;">subsample_limits_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subsample_group</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">    <span class="n" style="color: #333;">subsample_limits_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sequences-per-group'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"subsample to no more than this number of sequences per category"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python">    <span class="n" style="color: #333;">subsample_limits_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--subsample-max-sequences'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"subsample to no more than this number of sequences"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">    <span class="n" style="color: #333;">subsample_limits_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--subsample-max-sequences'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"subsample to no more than this number of sequences<span class="idiff left right">; can be used without the group_by argument</span>"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">    <span class="n" style="color: #333;">probabilistic_sampling_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subsample_group</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">    <span class="n" style="color: #333;">probabilistic_sampling_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--probabilistic-sampling'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Enable probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">    <span class="n" style="color: #333;">probabilistic_sampling_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--no-probabilistic-sampling'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_false'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'probabilistic_sampling'</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="348" style="width: 35px; color: rgba(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="348" style="width: 35px; color: rgba(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">@@ -348,9 +348,9 @@ def run(args):</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">        <span class="n" style="color: #333;">dates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_numerical_dates</span><span class="p">(</span><span class="n" style="color: #333;">meta_dict</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"%Y-%m-%d"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">        <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_keep</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python">            <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isscalar</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python">            <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isscalar</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span><span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python">            <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isscalar</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python">            <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">isscalar</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">dates</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">])</span><span class="o" style="font-weight: 600;"><<span class="idiff left right">=</span></span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">max_date</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">        <span class="n" style="color: #333;">num_excluded_by_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq_keep</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">        <span class="n" style="color: #333;">seq_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></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">@@ -376,7 +376,15 @@ def run(args):</td>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_seed</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python">        <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_seed</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python">    <span class="n" style="color: #333;">num_excluded_subsamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group_by</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences_per_group</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_max_sequences</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsample_max_sequences</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group_by</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences_per_group</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python">        </span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#set groups to group_by values</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group_by</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python">            <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group_by</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#if group_by not specified use dummy category</span></span>

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python">            <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"_dummy"</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">        <span class="n" style="color: #333;">spg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences_per_group</span></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">        <span class="n" style="color: #333;">seq_names_by_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"></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">@@ -384,8 +392,10 @@ def run(args):</td>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">            <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">            <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meta_dict</span><span class="p">[</span><span class="n" style="color: #333;">seq_name</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># collect group specifiers</span></span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group_by</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"_dummy"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python">                    <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

</pre>

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389

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">                    <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">])</span></span>

</pre>

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390

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'month'</span><span class="p">,</span> <span class="s" style="color: #d14;">'year'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'date'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="407" style="width: 35px; color: rgba(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="417" style="width: 35px; color: rgba(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">@@ -407,16 +417,16 @@ def run(args):</td>

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<td class="new_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

418

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#If didnt find any categories specified, all seqs will be in 'unknown' - but don't sample this!</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

409

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<td class="new_line diff-line-num" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

419

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq_names_by_group</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">'unknown'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_names_by_group</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="s" style="color: #d14;">'unknown'</span><span class="p">,)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_names_by_group</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="420" 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="LC410" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: The specified group-by categories (%s) were not found."</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">group<span class="idiff right">_by</span></span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: The specified group-by categories (%s) were not found."</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">group<span class="idiff left right">s</span></span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

421

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">                  <span class="s" style="color: #d14;">"No sequences-per-group sampling will be done."</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="422" 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="LC412" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">group<span class="idiff right">_by</span></span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span><span class="s" style="color: #d14;">'month'</span><span class="p">]]):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

422

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group<span class="idiff left right">s</span></span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span><span class="s" style="color: #d14;">'month'</span><span class="p">]]):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Note that using 'year' or 'year month' requires a column called 'date'."</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Check to see if some categories are missing to warn the user</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">            <span class="n" style="color: #333;">group_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">'date'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'year'</span><span class="p">,</span><span class="s" style="color: #d14;">'month'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cat</span></span>

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<td class="new_line diff-line-num old" data-linenumber="428" 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="LC418" class="line" lang="python">                            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">group<span class="idiff right">_by</span></span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">missing_cats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cat</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">meta_columns</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python">                            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group<span class="idiff left right">s</span></span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python">            <span class="n" style="color: #333;">missing_cats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cat</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">meta_columns</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cat</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"_dummy"</span></span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_cats</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING:"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'date'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cat</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_cats</span><span class="p">]):</span></span>

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<br>

</li>

<li id="104ddc27c2db78b040d33b5412a2de3d66f15177">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#104ddc27c2db78b040d33b5412a2de3d66f15177"><strong>augur/refine.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="222" style="width: 35px; color: rgba(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">@@ -222,7 +222,11 @@ def run(args):</td>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">                <span class="n" style="color: #333;">node_data</span><span class="p">[</span><span class="s" style="color: #d14;">'skyline'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">skyline</span><span class="p">.</span><span class="n" style="color: #333;">x</span><span class="p">],</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conf</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">                                        <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">skyline</span><span class="p">.</span><span class="n" style="color: #333;">y</span><span class="p">],</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">conf</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]]</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: skyline optimization by TreeTime has failed."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python">                    <span class="s" style="color: #d14;">"ERROR: skyline optimization by TreeTime has failed."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">                    <span class="s" style="color: #d14;">"To avoid this error, try running without coalescent optimization or with `--coalescent opt` instead of `--coalescent skyline`."</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">                <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">        <span class="n" style="color: #333;">attributes</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'numdate'</span><span class="p">,</span> <span class="s" style="color: #d14;">'clock_length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mutation_length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'raw_date'</span><span class="p">,</span> <span class="s" style="color: #d14;">'date'</span><span class="p">])</span></span>

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<br>

</li>

<li id="5aa84eddf9e5286c15160859a367e2b67129d7d8">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#5aa84eddf9e5286c15160859a367e2b67129d7d8"><strong>augur/tree.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(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">@@ -133,6 +133,10 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;">        aln_file    file name of input aligment</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;">        out_file    file name to write tree to</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;">    '''</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python">    <span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_executable</span><span class="p">([</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">        <span class="s" style="color: #d14;">"iqtree2"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">        <span class="s" style="color: #d14;">"iqtree"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python">    <span class="p">])</span></span>

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<td class="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># create a dictionary for characters that IQ-tree changes.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># we remove those prior to tree-building and reinstantiate later</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">random_string</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="188" style="width: 35px; color: rgba(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="192" style="width: 35px; color: rgba(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">@@ -188,10 +192,10 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt</td>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"none"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="195" 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="LC191" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left">"</span>iqtree<span class="idiff right">"</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">iqtree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">                <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="n" style="color: #333;">substitution_model</span><span class="p">,</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="198" 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="LC194" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left">"</span>iqtree<span class="idiff">"</span></span><span class="p"><span class="idiff right">,</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)]</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">        <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fast_opts</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nt"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">),</span> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">tmp_aln_file</span><span class="p">),</span> <span class="n" style="color: #333;">tree_builder_args</span><span class="p">,</span> <span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p">(</span><span class="n" style="color: #333;">log_file</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">    <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>

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<br>

</li>

<li id="0698fd06e0fd6334ba03f49c4d5fcab894112ff2">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#0698fd06e0fd6334ba03f49c4d5fcab894112ff2"><strong>tests/functional/filter.t</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(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="20" style="width: 35px; color: rgba(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">@@ -20,6 +20,22 @@ With 10 groups to subsample from, this should produce one sequence per group.</td>

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20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl">  <span class="o" style="font-weight: 600;">\</span><span class="sr" style="color: #009926;">s*10 (re)</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="sr" style="color: #009926;">  $ rm -f "$TMP/filtered.fasta"</span></span>

</pre>

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22

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22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"><span class="sr" style="color: #009926;">Filter with subsampling where no more than 5 sequences are requested and no groups are specified.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="sr" style="color: #009926;">This generates a dummy category and subsamples from there. With no-probabilistic-sampling we expect exactly 5 sequences.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="sr" style="color: #009926;">  $ ${AUGUR} filter \</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --sequences filter/sequences.fasta \</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --sequence-index filter/sequence_index.tsv \</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --metadata filter/metadata.tsv \</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --min-date 2012 \</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --subsample-max-sequences 5 \</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --subsample-seed 314159 \</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --no-probabilistic-sampling \</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"><span class="sr" style="color: #009926;">  >  --output "$TMP/filtered.fasta" > /dev/null</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

35

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="sr" style="color: #009926;">  $ grep ">" "$TMP/filtered.fasta" | wc -l</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="sr" style="color: #009926;">  \s*5 (re)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="sr" style="color: #009926;">  $ rm -f "$TMP/filtered.fasta"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="sr" style="color: #009926;">Try to filter with subsampling when there are more available groups than requested sequences.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="perl"><span class="sr" style="color: #009926;">This should fail, as probabilistic sampling is explicitly disabled.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f11f72e22ad9db7339f7290c375885f5e6f24b6c">

<a href="https://salsa.debian.org/med-team/augur/-/commit/d19d29e58828e426502c2411a61b05818fd67285#f11f72e22ad9db7339f7290c375885f5e6f24b6c"><strong>tests/test_filter.py</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">@@ -215,3 +215,31 @@ class TestFilter:</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">augur</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">        <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">out_fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SEQ_3"</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_run_min_date</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">argparser</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test that filter --min-date is inclusive"""</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python">        <span class="n" style="color: #333;">out_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"out.fasta"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python">        <span class="n" style="color: #333;">min_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-02-26"</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python">        <span class="n" style="color: #333;">meta_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_metadata</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="p">((</span><span class="s" style="color: #d14;">"strain"</span><span class="p">,</span><span class="s" style="color: #d14;">"date"</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-02-XX"</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-02-26"</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_3"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-02-25"</span><span class="p">)))</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">        <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparser</span><span class="p">(</span><span class="s" style="color: #d14;">'-s %s --metadata %s -o %s --min-date %s'</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">                         <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fasta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">meta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">out_fn</span><span class="p">,</span> <span class="n" style="color: #333;">min_date</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">        <span class="n" style="color: #333;">augur</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python">        <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">out_fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_filter_run_max_date</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">argparser</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test that filter --max-date is inclusive"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">        <span class="n" style="color: #333;">out_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"out.fasta"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python">        <span class="n" style="color: #333;">max_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-03-01"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">        <span class="n" style="color: #333;">meta_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_metadata</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="p">((</span><span class="s" style="color: #d14;">"strain"</span><span class="p">,</span><span class="s" style="color: #d14;">"date"</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-03-XX"</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-03-01"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">                                          <span class="p">(</span><span class="s" style="color: #d14;">"SEQ_3"</span><span class="p">,</span><span class="s" style="color: #d14;">"2020-03-02"</span><span class="p">)))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">        <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparser</span><span class="p">(</span><span class="s" style="color: #d14;">'-s %s --metadata %s -o %s --max-date %s'</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python">                         <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fasta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">meta_fn</span><span class="p">,</span> <span class="n" style="color: #333;">out_fn</span><span class="p">,</span> <span class="n" style="color: #333;">max_date</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python">        <span class="n" style="color: #333;">augur</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">        <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">out_fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"SEQ_1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"SEQ_2"</span><span class="p">]</span></span></pre>

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