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<h3>
Nilesh Patra pushed to branch master
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/b573127236dc968a9869d02d53177818701d8838">b5731272</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-25T18:49:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.0.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/66ab04369255f3ce975589e31ce41eb8f6f8a1f5">66ab0436</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-06T20:52:34+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/3288cbfb59baaf11594edb77c5e8fc93f0a112b6">3288cbfb</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-06T20:52:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 13.0.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/c075e9e68c7234f7b65c0b9492ebbff48dfc8364">c075e9e6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-06T20:53:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/13.0.1'
Update to upstream version '13.0.1'
with Debian dir 8e92d3d632d97b2ff177948bd90d500970c82ebd</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/fcc1149fce411013a2fae7486fabf91d92bdf5c8">fcc1149f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-06T20:53:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/augur/-/commit/5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7">5d3aafe8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-06T20:54:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">
augur/__version__.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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#e52131dead72c2fa2a845dc3c26000af292e89fe">
docs/faq/metadata.md
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<li class="file-stats">
<a href="#af160d50ba669524dae9392b05d5bb3914d02635">
tests/builds/various_export_settings/config/footer-description.md
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<li class="file-stats">
<a href="#0698fd06e0fd6334ba03f49c4d5fcab894112ff2">
tests/functional/filter.t
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</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#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 +3,16 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.1 (1 October 2021)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="8" 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="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<td class="new_line diff-line-num new" data-linenumber="9" 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="LC9" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="10" 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="LC10" class="line" lang="markdown"><span class="p">*</span> docs: Fix broken link to latitude/longitude documentation. <span class="p">[</span><span class="nv" style="color: #008080;">#766</span><span class="p">][]</span> (@victorlin)</span>
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<td class="new_line diff-line-num new" data-linenumber="11" 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="LC11" class="line" lang="markdown"><span class="p">*</span> filter: Fix reproducibility of subsampling by using the user-defined random seed in all random function calls and by ordering strain sets as lists prior to adding strains to group-by priority queues. <span class="p">[</span><span class="nv" style="color: #008080;">#772</span><span class="p">][]</span> (@huddlej)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="13" 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="LC13" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#766</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/766</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" 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="LC14" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#772</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/772</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 13.0.0 (17 August 2021)</span></span>
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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(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="LC17" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Major Changes</span></span>
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<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">
<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>
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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;">'13.0.<span class="idiff left right">0</span>'</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;">'13.0.<span class="idiff left right">1</span>'</span></span>
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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>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#1058ed03848375e3c1a8b82623654cb578984455"><strong>augur/filter.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1049" style="width: 35px; color: rgba(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">@@ -1049,7 +1049,7 @@ class PriorityQueue:</td>
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1049
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">item</span></span>
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1050
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1052" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_queues_by_group</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">,</span> <span class="n" style="color: #333;">max_attempts</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_queues_by_group</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">,</span> <span class="n" style="color: #333;">max_attempts</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">random_seed</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="python"> <span class="s" style="color: #d14;">"""Create a dictionary of priority queues per group for the given maximum size.</span></span>
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="python"><span class="s" style="color: #d14;"> When the maximum size is fractional, probabilistically sample the maximum</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">@@ -1067,24 +1067,32 @@ def create_queues_by_group(groups, max_size, max_attempts=100):</td>
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1067
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="python"><span class="s" style="color: #d14;"> Create queues for two groups with a fractional maximum size. Their total max</span></span>
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1068
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="python"><span class="s" style="color: #d14;"> size should still be an integer value greater than zero.</span></span>
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1069
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="python"></span>
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1070
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="python"><span class="s" style="color: #d14;"> >>> queues = create_queues_by_group(groups, 0.1)</span></span>
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="python"><span class="s" style="color: #d14;"> >>> seed = 314159</span></span>
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="python"><span class="s" style="color: #d14;"> >>> queues = create_queues_by_group(groups, 0.1, random_seed=seed)</span></span>
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="python"><span class="s" style="color: #d14;"> >>> int(sum(queue.max_size for queue in queues.values())) > 0</span></span>
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1073
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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="python"><span class="s" style="color: #d14;"> True</span></span>
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1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="python"><span class="s" style="color: #d14;"> A subsequent run of this function with the same groups and random seed</span></span>
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="python"><span class="s" style="color: #d14;"> should produce the same queues and queue sizes.</span></span>
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="python"><span class="s" style="color: #d14;"> >>> more_queues = create_queues_by_group(groups, 0.1, random_seed=seed)</span></span>
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="python"><span class="s" style="color: #d14;"> >>> [queue.max_size for queue in queues.values()] == [queue.max_size for queue in more_queues.values()]</span></span>
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="python"><span class="s" style="color: #d14;"> True</span></span>
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="python"> <span class="n" style="color: #333;">queues_by_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="LC1084" class="line" lang="python"> <span class="n" style="color: #333;">total_max_size</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="LC1085" class="line" lang="python"> <span class="n" style="color: #333;">attempts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1080" class="line" lang="python"> <span class="n" style="color: #333;">random_generator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">default_rng</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="python"> <span class="n" style="color: #333;">random_generator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">default_rng</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">random_seed</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For small fractional maximum sizes, it is possible to randomly select</span></span>
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maximum queue sizes that all equal zero. When this happens, filtering</span></span>
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fails unexpectedly. We make multiple attempts to create queues with</span></span>
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maximum sizes greater than zero for at least one queue.</span></span>
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">total_max_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">attempts</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_attempts</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1087" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</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="LC1095" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">groups</span><span class="p"><span class="idiff right">)</span>:</span></span>
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1088
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span><span class="p">:</span></span>
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1089
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="python"> <span class="n" style="color: #333;">queue_max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random_generator</span><span class="p">.</span><span class="n" style="color: #333;">poisson</span><span class="p">(</span><span class="n" style="color: #333;">max_size</span><span class="p">)</span></span>
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1090
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1428" style="width: 35px; color: rgba(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="1436" style="width: 35px; color: rgba(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">@@ -1428,10 +1436,11 @@ def run(args):</td>
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1428
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">queues_by_group</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1429
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1437
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="python"> <span class="n" style="color: #333;">queues_by_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1430
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1438
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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="python"></span>
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1431
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<pre style="margin: 0;">-<span id="LC1431" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">group</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;">group_by_strain</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff right">item</span>s</span><span class="p">():</span></span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">group_by_strain</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff">key</span>s</span><span class="p">()<span class="idiff right">)</span>:</span></span>
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1432
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1440
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># During this first pass, we do not know all possible</span></span>
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1433
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1441
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># groups will be, so we need to build each group's queue</span></span>
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1434
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1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># as we first encounter the group.</span></span>
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1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">]</span></span>
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1435
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group</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;">queues_by_group</span><span class="p">:</span></span>
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1436
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="python"> <span class="n" style="color: #333;">queues_by_group</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PriorityQueue</span><span class="p">(</span></span>
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1437
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="python"> <span class="n" style="color: #333;">max_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sequences_per_group</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1501" style="width: 35px; color: rgba(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="1510" style="width: 35px; color: rgba(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">@@ -1501,6 +1510,7 @@ def run(args):</td>
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1501
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1510
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="python"> <span class="n" style="color: #333;">queues_by_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create_queues_by_group</span><span class="p">(</span></span>
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1502
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1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="python"> <span class="n" style="color: #333;">records_per_group</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span></span>
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1503
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1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="python"> <span class="n" style="color: #333;">sequences_per_group</span><span class="p">,</span></span>
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1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="python"> <span class="n" style="color: #333;">random_seed</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;">subsample_seed</span><span class="p">,</span></span>
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1504
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1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="python"> <span class="p">)</span></span>
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1505
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1515
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make a second pass through the metadata, only considering records that</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">@@ -1522,7 +1532,8 @@ def run(args):</td>
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="python"> <span class="n" style="color: #333;">group_by</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1525" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span><span class="p">,</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strain</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">group_by_strain</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_by_strain</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC1537" class="line" lang="python"> <span class="n" style="color: #333;">queues_by_group</span><span class="p">[</span><span class="n" style="color: #333;">group</span><span class="p">].</span><span class="n" style="color: #333;">add</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="python"> <span class="n" style="color: #333;">priorities</span><span class="p">[</span><span class="n" style="color: #333;">strain</span><span class="p">],</span></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">augur (13.0.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Wed, 06 Oct 2021 20:54:16 +0530</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">augur (13.0.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Update manpage</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-freezegun <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> vcftools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-xopen</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/augur</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/augur.git</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Homepage: https://github.com/nextstrain/augur</span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#e52131dead72c2fa2a845dc3c26000af292e89fe"><strong>docs/faq/metadata.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">@@ -37,7 +37,7 @@ Geographic locations can be broken down, for example, into `region`, `country`,</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">It is important that these are spelled consistently.</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">If you want to include locations where augur doesn't know the lat-long values, you can include them - see how <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">lat_longs</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">If you want to include locations where augur doesn't know the lat-long values, you can include them - see how <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;"><span class="idiff left">./</span>lat_longs<span class="idiff right">.html</span></span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Consistancy and Style</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#af160d50ba669524dae9392b05d5bb3914d02635"><strong>tests/builds/various_export_settings/config/footer-description.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">@@ -16,8 +16,6 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">external link</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com</span><span class="p">)</span> should open in a new tab.</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="nt" style="color: #000080;"><script></span>alert("Do bad things")<span class="nt" style="color: #000080;"></script></span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">horizontal</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">***</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,4 +39,3 @@ Markdown image renders as a centered image:</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown">Multiple images with one or no line breaks are centered together:</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Markdown img</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/static/nextstrain-logo-small.ea8c3e13.png</span><span class="p">)</span>](https://nextstrain.org)<span class="p">[</span><span class="nv" style="color: #008080;">![Markdown img</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/static/nextstrain-logo-small.ea8c3e13.png</span><span class="p">)</span>](https://nextstrain.org)</span></pre>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"></span></pre>
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<a href="https://salsa.debian.org/med-team/augur/-/compare/a1af33399a852735b5cdd1477eb9ccc1b1718fd0...5d3aafe8e5bb9a72ca7b4f96e9505dff6ba477a7#0698fd06e0fd6334ba03f49c4d5fcab894112ff2"><strong>tests/functional/filter.t</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">@@ -22,10 +22,22 @@ Filter with subsampling, requesting 1 sequence per group (for a group with 4 dis</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --metadata filter/metadata.tsv \</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --group-by region \</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --sequences-per-group 1 \</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-seed 314159 \</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output-strains "$TMP/filtered_strains.txt" > /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ wc -l "$TMP/filtered_strains.txt"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="sr" style="color: #009926;"> \s*</span><span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">.*</span> <span class="p">(</span><span class="nv" style="color: #008080;">re</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span> <span class="nv" style="color: #008080;">rm</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains.txt</span><span class="p">"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"><span class="nv" style="color: #008080;">By</span> <span class="nv" style="color: #008080;">setting</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">subsample</span> <span class="nv" style="color: #008080;">seed</span> <span class="nv" style="color: #008080;">above</span><span class="p">,</span> <span class="nv" style="color: #008080;">we</span> <span class="nv" style="color: #008080;">should</span> <span class="nv" style="color: #008080;">guarantee</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">we</span> <span class="nv" style="color: #008080;">get</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">same</span> <span class="p">"</span><span class="s2" style="color: #d14;">random</span><span class="p">"</span> <span class="nv" style="color: #008080;">strains</span> <span class="nv" style="color: #008080;">as</span> <span class="nv" style="color: #008080;">another</span> <span class="nv" style="color: #008080;">run</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">same</span> <span class="nv" style="color: #008080;">command</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span> <span class="nv" style="color: #008080;">$</span><span class="p">{</span><span class="nv" style="color: #008080;">AUGUR</span><span class="p">}</span> <span class="nv" style="color: #008080;">filter</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">metadata</span> <span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">tsv</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">group</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">by</span> <span class="nv" style="color: #008080;">region</span> <span class="o" style="font-weight: 600;">\</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">sequences</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">per</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">group</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">\</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">subsample</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">output</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">strains</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains_repeated.txt</span><span class="p">"</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span> <span class="nv" style="color: #008080;">diff</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">u</span> <span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains.txt</span><span class="p">")</span> <span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains_repeated.txt</span><span class="p">")</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span> <span class="nv" style="color: #008080;">rm</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains.txt</span><span class="p">"</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/filtered_strains_repeated.txt</span><span class="p">"</span></span>
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29
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"></span>
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30
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="perl"><span class="nv" style="color: #008080;">Filter</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">subsampling</span><span class="p">,</span> <span class="nv" style="color: #008080;">requesting</span> <span class="nb" style="color: #0086b3;">no</span> <span class="nv" style="color: #008080;">more</span> <span class="nv" style="color: #008080;">than</span> <span class="mi" style="color: #099;">8</span> <span class="nv" style="color: #008080;">sequences</span><span class="o" style="font-weight: 600;">.</span></span>
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31
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"><span class="nv" style="color: #008080;">With</span> <span class="mi" style="color: #099;">8</span> <span class="nv" style="color: #008080;">groups</span> <span class="nv" style="color: #008080;">to</span> <span class="nv" style="color: #008080;">subsample</span> <span class="nv" style="color: #008080;">from</span> <span class="p">(</span><span class="nv" style="color: #008080;">after</span> <span class="nv" style="color: #008080;">filtering</span><span class="p">),</span> <span class="nv" style="color: #008080;">this</span> <span class="nv" style="color: #008080;">should</span> <span class="nv" style="color: #008080;">produce</span> <span class="nv" style="color: #008080;">one</span> <span class="nv" style="color: #008080;">sequence</span> <span class="nv" style="color: #008080;">per</span> <span class="nv" style="color: #008080;">group</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,8 +100,7 @@ Explicitly use probabilistic subsampling to handle the case when there are more</td>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-max-sequences 5 \</span></span>
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89
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-seed 314159 \</span></span>
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90
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --probabilistic-sampling \</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output "$TMP/filtered.fasta" > /dev/null</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ rm -f "$TMP/filtered.fasta"</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output-strains "$TMP/filtered_strains_probabilistic.txt" > /dev/null</span></span>
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93
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"></span>
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94
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="sr" style="color: #009926;">Using the default probabilistic subsampling, should work the same as the previous case.</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="112" style="width: 35px; color: rgba(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">@@ -101,8 +112,12 @@ Using the default probabilistic subsampling, should work the same as the previou</td>
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101
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --group-by country year month \</span></span>
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102
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-max-sequences 5 \</span></span>
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103
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --subsample-seed 314159 \</span></span>
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<td class="old_line diff-line-num old" data-linenumber="104" 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">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output "$TMP/filtered.fasta" > /dev/null</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ rm -f "$TMP/filtered.fasta"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"><span class="sr" style="color: #009926;"> > --output-strains "$TMP/filtered_strains_default.txt" > /dev/null</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"><span class="sr" style="color: #009926;">By setting the subsample seed above, we should get the same results for both runs.</span></span>
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<td class="old_line diff-line-num new" data-linenumber="106" 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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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ diff -u <(sort "$TMP/filtered_strains_probabilistic.txt") <(sort "$TMP/filtered_strains_default.txt")</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"><span class="sr" style="color: #009926;"> $ rm -f "$TMP/filtered_strains_probabilistic.txt" "$TMP/filtered_strains_default.txt"</span></span>
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106
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"></span>
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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"><span class="sr" style="color: #009926;">Filter using only metadata without sequence input or output and save results as filtered metadata.</span></span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl"></span>
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