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GitLab

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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/4b456b7906192b5c0a9dc2f0de027e3a021f82f4">4b456b79</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2020-11-19T01:45:17+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.1.1</pre>

</li>

</ul>

<h4>24 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

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<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#a1a05fb3eb681edc11e8c987f65967f416af0ee1">

augur/__version__.py

</a>

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<li class="file-stats">

<a href="#1058ed03848375e3c1a8b82623654cb578984455">

augur/filter.py

</a>

</li>

<li class="file-stats">

<a href="#0d0305472fcbc5cf656b5d71a25dfd30c8c8d131">

augur/utils.py

</a>

</li>

<li class="file-stats">

<a href="#254a2da7a740675e537439eb88e32083b9ea4771">

docs/conf.py

</a>

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<li class="file-stats">

<a href="#73cc809ba2916206462a7eb6005867f214a34fcc">

DEV_DOCS.md

→

docs/contribute/DEV_DOCS.md

</a>

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<li class="file-stats">

<a href="#6848655bfa8b3fad04eab5ecb4fe05d5ee158df6">

<span class="deleted-file">

−

docs/faq/augur_snakemake.md

</span>

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<li class="file-stats">

<a href="#16323572c1a0d9ce888f2b9e60ec666d09559810">

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−

docs/faq/community_hosting.md

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<li class="file-stats">

<a href="#59b1d7e40fede8c024a49e831a67e1ed941f50de">

docs/faq/faq.rst

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<a href="#474e2dee886fb77962b12d4e381b9ca22fa7c00c">

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+

docs/faq/what-is-a-build.md

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<li class="file-stats">

<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">

docs/index.rst

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<li class="file-stats">

<a href="#e8b985c0ef42231b85fdf9aa97fbad5fff94be7f">

docs/releases/migrating-v5-v6.md

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<li class="file-stats">

<a href="#1f374f74b0b9c0ebde03840d6c75d5e2e9f516de">

docs/releases/v6.md

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<li class="file-stats">

<a href="#6ceb651c15e9f3ce63e7396537e81e5b1377b418">

docs/tutorials/tb_tutorial.md

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<a href="#c82653f427e53da3edca7577d17b03fa3a909b8b">

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−

docs/tutorials/tutorials.rst

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<li class="file-stats">

<a href="#117e91c7f77ddab94ba103f3fddbb7e10ec356e7">

docs/tutorials/zika_tutorial.md

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<li class="file-stats">

<a href="#d6d5362abd39a9db0355122f2f394a267d81513f">

docs/usage/cli/filter.rst

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<li class="file-stats">

<a href="#51dfac45ef9ee65b645bb4efa64dc86e4d8c2c3b">

docs/usage/usage.rst

</a>

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

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<li class="file-stats">

<a href="#6788c84297b185802f92db51db36c33eb731ecfe">

tests/builds/zika.t

</a>

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<li class="file-stats">

<a href="#d765401a067b8ae8f8d883fc416c80ca1d23904f">

tests/functional/ancestral.t

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<li class="file-stats">

<a href="#9753651334e00be71d51aba2fccf83cd1d0508c5">

tests/functional/refine.t

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<li class="file-stats">

<a href="#dc10ba1af84013a385b35192d66ceb8036cefb1d">

tests/test_utils.py

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<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,6 +3,25 @@</td>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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4

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="5" 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">

5

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

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.1.1 (16 November 2020)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="7" 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">

7

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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="LC7" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

8

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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="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

9

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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="LC9" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> dependencies: Require the most recent minor versions of TreeTime (0.8.X) to fix numpy matrix errors <span class="p">[</span><span class="nv" style="color: #008080;">#633</span><span class="p">][]</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

11

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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="LC11" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="12" 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">

12

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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="LC12" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#633</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/633</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

13

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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="LC13" class="line" lang="markdown"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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="gu" style="color: #800080; font-weight: 600;">## 10.1.0 (13 November 2020)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

15

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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="LC15" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="16" 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">

16

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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>

</pre>

</td>

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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> docs: Migrate non-reference documentation to docs.nextstrain.org <span class="p">[</span><span class="nv" style="color: #008080;">#620</span><span class="p">][]</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> filter: Add <span class="sb" style="color: #d14;">`--exclude-ambiguous-dates-by`</span> flag to enable exclusion of samples with ambiguous dates <span class="p">[</span><span class="nv" style="color: #008080;">#623</span><span class="p">][]</span> and <span class="p">[</span><span class="nv" style="color: #008080;">#631</span><span class="p">][]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" 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><span class="ss" style="color: #990073;">#620</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/620</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">#623</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/623</span></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;">#631</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/nextstrain/augur/pull/631</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 10.0.4 (6 November 2020)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>

</pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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="28" 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="28" 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">@@ -28,7 +28,7 @@ The output of augur is a series of JSONs that can be used to visualize your resu</td>

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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Technical documentation for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain-augur.readthedocs.io/en/stable/installation/installation.html</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" 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="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Contributor guide</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="diff-line-num new_line" data-linenumber="30" 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="LC30" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Project board with available issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/orgs/nextstrain/projects/6</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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="diff-line-num new_line old" data-linenumber="31" 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="LC31" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Developer docs for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">./DEV_DOCS.md</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Developer docs for Augur</span><span class="p">](</span><span class="sx" style="color: #d14;">./<span class="idiff left right">docs/contribute/</span>DEV_DOCS.md</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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="diff-line-num new_line" data-linenumber="32" 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="LC32" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quickstart</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="34" 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="LC34" class="line" lang="markdown"></span>

</pre>

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<br>

</li>

<li id="a1a05fb3eb681edc11e8c987f65967f416af0ee1">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#a1a05fb3eb681edc11e8c987f65967f416af0ee1"><strong>augur/__version__.py</strong></a>

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<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="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;">'10.<span class="idiff left right">0.4</span>'</span></span>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1" 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="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;">'10.<span class="idiff left right">1.1</span>'</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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="diff-line-num new_line" data-linenumber="3" 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="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num new_line" data-linenumber="4" 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="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="1058ed03848375e3c1a8b82623654cb578984455">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#1058ed03848375e3c1a8b82623654cb578984455"><strong>augur/filter.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" 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="10" 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">@@ -10,7 +10,7 @@ import numpy as np</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">treetime.utils</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">get_numerical_dates</span><span class="p">,</span> <span class="n" style="color: #333;">run_shell_command</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span></span>

</pre>

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<td class="diff-line-num new new_line" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">get_numerical_dates</span><span class="p">,</span> <span class="n" style="color: #333;">run_shell_command</span><span class="p">,</span> <span class="n" style="color: #333;">shquote</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">is_date_ambiguous</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" 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="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">comment_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'#'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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="LC16" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,6 +105,8 @@ def register_arguments(parser):</td>

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<pre style="margin: 0;"> <span id="LC105" 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 samples matching these conditions. Ex: </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">host=rat</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> or </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">host!=rat</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">. Multiple values are processed as OR (matching any of those specified will be excluded), not AND"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--include-where'</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>

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<pre style="margin: 0;"> <span id="LC107" 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;">"Include samples with these values. ex: host=rat. Multiple values are processed as OR (having any of those specified will be included), not AND. This rule is applied last and ensures any sequences matching these rules will be included."</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;">parser</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="LC109" 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="LC110" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--query'</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;">"Filter samples by attribute. Uses Pandas Dataframe querying, see https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#indexing-query for syntax."</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;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</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;">"output file"</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">            <span class="n" style="color: #333;">num_excluded_by_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;">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;">seq_keep_by_length</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC234" 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;">seq_keep_by_length</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># filter by ambiguous dates</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">    <span class="n" style="color: #333;">num_excluded_by_ambiguous_date</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="LC238" 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;">exclude_ambiguous_dates_by</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;">meta_columns</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python">        <span class="n" style="color: #333;">seq_keep_by_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_keep</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC241" 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;">is_date_ambiguous</span><span class="p">(</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 class="s" style="color: #d14;">'date'</span><span class="p">],</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">exclude_ambiguous_dates_by</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python">                <span class="n" style="color: #333;">seq_keep_by_date</span><span class="p">.</span><span class="n" style="color: #333;">append</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="LC243" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">        <span class="n" style="color: #333;">num_excluded_by_ambiguous_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;">seq_keep_by_date</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" 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="n" style="color: #333;">seq_keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_keep_by_date</span></span>

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<td class="diff-line-num new new_line" data-linenumber="246" 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="LC246" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="247" 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="LC247" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># filter by date</span></span>

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<pre style="margin: 0;"> <span id="LC248" 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="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</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;">max_date</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;">meta_columns</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -423,6 +436,8 @@ def run(args):</td>

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<pre style="margin: 0;"> <span id="LC436" 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;">\t</span><span class="s" style="color: #d14;">%i of these were filtered out by the query:</span><span class="se" style="color: #d14;">\n\t\t\"</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">num_excluded_by_query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC437" 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_length</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="438" 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="LC438" 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;">\t</span><span class="s" style="color: #d14;">%i of these were dropped because they were shorter than minimum length of %sbp"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">num_excluded_by_length</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_length</span><span class="p">))</span></span>

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<td class="diff-line-num new new_line" data-linenumber="439" 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="LC439" 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;">exclude_ambiguous_dates_by</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">num_excluded_by_ambiguous_date</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="440" 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="LC440" 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;">\t</span><span class="s" style="color: #d14;">%i of these were dropped because of their ambiguous date in %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">num_excluded_by_ambiguous_date</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">exclude_ambiguous_dates_by</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_date</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;">max_date</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;">meta_columns</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC442" 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;">\t</span><span class="s" style="color: #d14;">%i of these were dropped because of their date (or lack of date)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">num_excluded_by_date</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC443" 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;">non_nucleotide</span><span class="p">:</span></span>

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<li id="0d0305472fcbc5cf656b5d71a25dfd30c8c8d131">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#0d0305472fcbc5cf656b5d71a25dfd30c8c8d131"><strong>augur/utils.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">@@ -73,6 +73,37 @@ def ambiguous_date_to_date_range(uncertain_date, fmt, min_max_year=None):</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_metadata</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MetadataFile</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_date_ambiguous</span><span class="p">(</span><span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="n" style="color: #333;">ambiguous_by</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"any"</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;">    Returns whether a given date string in the format of YYYY-MM-DD is ambiguous by a given part of the date (e.g., day, month, year, or any parts).</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;">    date : str</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;">        Date string in the format of YYYY-MM-DD</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;">    ambiguous_by : str</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;">        Field of the date string to test for ambiguity ("day", "month", "year", "any")</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">    <span class="n" style="color: #333;">date_components</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</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="LC88" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC89" 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;">date_components</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">year</span><span class="p">,</span> <span class="n" style="color: #333;">month</span><span class="p">,</span> <span class="n" style="color: #333;">day</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">date_components</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">date_components</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="python">        <span class="n" style="color: #333;">year</span><span class="p">,</span> <span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">date_components</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" 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="LC93" class="line" lang="python">        <span class="n" style="color: #333;">day</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"XX"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" 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="diff-line-num new new_line" data-linenumber="95" 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="LC95" class="line" lang="python">        <span class="n" style="color: #333;">year</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">date_components</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="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python">        <span class="n" style="color: #333;">month</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"XX"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python">        <span class="n" style="color: #333;">day</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"XX"</span></span>

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<td class="diff-line-num new new_line" data-linenumber="98" 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="LC98" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="99" 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="LC99" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Determine ambiguity hierarchically such that, for example, an ambiguous</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" 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="LC100" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># month implicates an ambiguous day even when day information is available.</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">((</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python">        <span class="s" style="color: #d14;">"X"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">year</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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="LC103" class="line" lang="python">        <span class="s" style="color: #d14;">"X"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">month</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ambiguous_by</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"any"</span><span class="p">,</span> <span class="s" style="color: #d14;">"month"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">),</span></span>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="python">        <span class="s" style="color: #d14;">"X"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">day</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ambiguous_by</span> <span class="ow" style="font-weight: 600;">in</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>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">    <span class="p">))</span></span>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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;">name_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">date_col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">min_max_year</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fmt</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>

</pre>

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<br>

</li>

<li id="254a2da7a740675e537439eb88e32083b9ea4771">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" 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="53" 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">@@ -53,7 +53,7 @@ author = prose_list(git_authors())</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any Sphinx extension module names here, as strings. They can be</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># extensions coming with Sphinx (named 'sphinx.ext.*') or your custom</span></span>

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<td class="diff-line-num old_line" data-linenumber="55" 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="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ones.</span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'recommonmark'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx.ext.autodoc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinxarg.ext'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx.ext.napoleon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx_markdown_tables'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'recommonmark'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx.ext.autodoc'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinxarg.ext'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx.ext.napoleon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx_markdown_tables'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'sphinx.ext.intersphinx'</span></span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="57" 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="LC57" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="58" 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="diff-line-num new_line" data-linenumber="58" 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="LC58" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="n" style="color: #333;">templates_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_templates'</span><span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="61" 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">@@ -61,7 +61,19 @@ templates_path = ['_templates']</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># List of patterns, relative to source directory, that match files and</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directories to ignore when looking for source files.</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This pattern also affects html_static_path and html_extra_path.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="LC64" class="line" lang="python"><span class="n" style="color: #333;">exclude_patterns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_build'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Thumbs.db'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.DS_Store'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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="LC64" class="line" lang="python"><span class="n" style="color: #333;">exclude_patterns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_build'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Thumbs.db'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.DS_Store'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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="LC65" class="line" lang="python">    <span class="s" style="color: #d14;">'contribute/DEV_DOCS.md'</span><span class="p">,</span></span>

</pre>

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66

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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="LC66" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/colors.md'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" 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">

67

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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="LC67" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/fasta_input.md'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" 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">

68

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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="LC68" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/import-beast.md'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" 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">

69

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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="LC69" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/lat_longs.md'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" 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">

70

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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="LC70" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/seq_traits.md'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" 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">

71

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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="LC71" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/translate_ref.md'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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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72

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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="LC72" class="line" lang="python">    <span class="s" style="color: #d14;">'faq/vcf_input.md'</span><span class="p">,</span></span>

</pre>

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73

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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="LC73" class="line" lang="python">    <span class="s" style="color: #d14;">'tutorials/tb_tutorial.md'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" 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">

74

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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="LC74" class="line" lang="python">    <span class="s" style="color: #d14;">'tutorials/zika_tutorial.md'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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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75

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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="LC75" class="line" lang="python">    <span class="s" style="color: #d14;">'usage/augur_snakemake.md'</span><span class="p">,</span></span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" 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">

65

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<td class="diff-line-num new_line" data-linenumber="77" 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">

77

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" 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">

66

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<td class="diff-line-num new_line" data-linenumber="78" 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">

78

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

<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># A string of reStructuredText that will be included at the end of every source</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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">

67

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<td class="diff-line-num new_line" data-linenumber="79" 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">

79

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

<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file that is read. This is a possible place to add substitutions that should</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="90" 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">@@ -78,6 +90,12 @@ rst_epilog = f"""</td>

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78

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<td class="diff-line-num new_line" data-linenumber="90" 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">

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" 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">

79

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<td class="diff-line-num new_line" data-linenumber="91" 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">

91

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

<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="n" style="color: #333;">html_theme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'nextstrain-sphinx-theme'</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="80" 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="diff-line-num new_line" data-linenumber="92" 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">

92

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

<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="93" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="n" style="color: #333;">html_theme_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="python">    <span class="s" style="color: #d14;">'logo_only'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># if True, don't display project name at top of the sidebar</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" 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="LC95" class="line" lang="python">    <span class="s" style="color: #d14;">'collapse_navigation'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># if True, no [+] icons in sidebar</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python">    <span class="s" style="color: #d14;">'titles_only'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># if True, page subheadings not included in nav</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" 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="LC97" class="line" lang="python"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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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="LC98" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" 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">

81

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain custom static files (such as style sheets) here,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" 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">

82

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<td class="diff-line-num new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># relative to this directory. They are copied after the builtin static files,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" 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">

83

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<td class="diff-line-num new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># so a file named "default.css" will overwrite the builtin "default.css".</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" 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="106" 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">@@ -88,3 +106,9 @@ html_static_path = ['_static']</td>

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<td class="diff-line-num old_line" data-linenumber="88" 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">

88

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<td class="diff-line-num new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="n" style="color: #333;">html_css_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="89" 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">

89

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">    <span class="s" style="color: #d14;">'css/custom.css'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="90" 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">

90

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Cross-project references ------------------------------------------------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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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="LC112" class="line" lang="python"><span class="n" style="color: #333;">intersphinx_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="python">    <span class="s" style="color: #d14;">'docs.nextstrain.org'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'https://docs.nextstrain.org/en/latest/'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="python"><span class="p">}</span></span></pre>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Development Docs for Contributors</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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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="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># <span class="idiff left right">Augur </span>Development Docs for Contributors</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

2

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<td class="diff-line-num new_line" 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">

2

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

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="markdown">Thank you for helping us to improve <span class="idiff left right">Nextstrain</span>! This document describes:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Thank you for helping us to improve <span class="idiff left right">Augur</span>! This document describes:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="markdown"><span class="p">-</span> Getting Started</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">-</span> Contributing code</span>

</pre>

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<br>

</li>

<li id="6848655bfa8b3fad04eab5ecb4fe05d5ee158df6">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#6848655bfa8b3fad04eab5ecb4fe05d5ee158df6"><strong>docs/faq/augur_snakemake.md</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown">../usage/augur_snakemake.md</span></pre>

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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">\ No newline at end of file</td>

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<br>

</li>

<li id="16323572c1a0d9ce888f2b9e60ec666d09559810">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#16323572c1a0d9ce888f2b9e60ec666d09559810"><strong>docs/faq/community_hosting.md</strong>

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Sharing your analysis</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">nextstrain.org</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org</span><span class="p">)</span> has a feature that allows you to share your own analysis through the nextstrain.org website.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">This works using github as a repository for your analysis files.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">To share an analysis, you need to create a repository.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">The name of the repository will be what is used to access the results.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">Within this repository, there should a folder called auspice which contains the output json files of the augur pipeline.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">Importantly, the name of these files has to start with the name of the repository.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">If so, you should be able to access your analysis via the nextstrain community feature.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">As an example, lets look at one of our nextstrain community analysis.</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">The following link shows you an analysis we made a few month ago of many influenza B sequences:</span>

</pre>

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

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

</pre>

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</tr>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">nextstrain.org/community/neherlab/allflu/B_ha</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/community/neherlab/allflu/B_ha</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">The analysis files are hosted on our github page in the reposity</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">github.com/neherlab/allflu</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/neherlab/allflu</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">In this repository, you'll find the folder <span class="sb" style="color: #d14;">`auspice`</span> which contains the files</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">allflu_B_ha_meta.json</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown">allflu_B_ha_tree.json</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">Note that all files start with "allflu" which matches the name of the repository.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">In fact, there are multiple analysis in this folder. The corresponding files all start with "allflu" but they differ in the viral lineage they correspond to:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">allflu_B_ha_meta.json</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">allflu_B_ha_tree.json</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown">allflu_h1n1_ha_meta.json</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown">allflu_h1n1_ha_tree.json</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">allflu_h1n1pdm_ha_meta.json</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">allflu_h1n1pdm_ha_tree.json</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="34" 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">

34

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">allflu_h3n2_ha_meta.json</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">allflu_h3n2_ha_tree.json</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">All these can be accessed as</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

</td>

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">nextstrain.org/community/neherlab/allflu/h1n1_ha</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/community/neherlab/allflu/h1n1_ha</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">nextstrain.org/community/neherlab/allflu/h3n2_ha</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/community/neherlab/allflu/h3n2_ha</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="42" 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">

42

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">nextstrain.org/community/neherlab/allflu/h1n1pdm_ha</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nextstrain.org/community/neherlab/allflu/h1n1pdm_ha</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="44" 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">

44

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="59b1d7e40fede8c024a49e831a67e1ed941f50de">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#59b1d7e40fede8c024a49e831a67e1ed941f50de"><strong>docs/faq/faq.rst</strong></a>

<hr>

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

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" 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="10" 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">@@ -10,15 +10,7 @@ common questions and problems users run into.</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" 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">

10

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">   :maxdepth: 1</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

</td>

<td class="diff-line-num new_line" data-linenumber="11" 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">

11

</td>

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

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

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="12" 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">

12

</td>

<td class="diff-line-num new_line" data-linenumber="12" 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">

12

</td>

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">   what-is-a-build</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="13" 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">

13

</td>

<td class="diff-line-num new_line" data-linenumber="14" 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">

14

</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">   metadata</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="15" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">   translate_ref</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="15" 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">

15

</td>

<td class="diff-line-num new_line" data-linenumber="15" 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">

15

</td>

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="16" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">   community_hosting</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="16" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">   import-beast</span>

</pre>

</td>

</tr>

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18

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<td class="diff-line-num new_line old" data-linenumber="16" 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">

</td>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">   colors</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line old" data-linenumber="16" 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">

</td>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">   lat_longs</span>

</pre>

</td>

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<td class="diff-line-num 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">

20

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">   Specifying `refine` rates <refine></span></pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC21" class="line" lang="plaintext">   Using Augur and Snakemake <augur_snakemake></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="17" 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">

</td>

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC23" class="line" lang="plaintext">   fasta_input</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC24" class="line" lang="plaintext">   seq_traits</span></pre>

</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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">\ No newline at end of file</td>

</tr>

</table>

<br>

</li>

<li id="474e2dee886fb77962b12d4e381b9ca22fa7c00c">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#474e2dee886fb77962b12d4e381b9ca22fa7c00c"><strong>docs/faq/what-is-a-build.md</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># The concept of a 'build'</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Nextstrain's focus on providing a _real-time_ snapshot of evolving pathogen populations necessitates a reproducible analysis that can be rerun when new sequences are available.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">The individual steps necessary to repeat analysis together comprise a "build".</span>

</pre>

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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>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Because no two datasets or pathogens are the same, we build Augur to be flexible and suitable for different analyses.</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">The individual Augur commands are composable, and can be mixed and matched with other scripts as needed.</span>

</pre>

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">These steps, taken together, are what we refer to as a "build".</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

</pre>

</td>

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

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">The <span class="p">[</span><span class="nv" style="color: #008080;">Zika virus tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.nextstrain.org/en/latest/tutorials/zika.html#build-steps</span><span class="p">)</span> describes a build which contains the following steps:</span>

</pre>

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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="p">1.</span> Prepare pathogen sequences and metadata</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">2.</span> Align sequences</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">3.</span> Construct a phylogeny from aligned sequences</span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">4.</span> Annotate the phylogeny with inferred ancestral pathogen dates, sequences, and traits</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">5.</span> Export the annotated phylogeny and corresponding metadata into auspice-readable format</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">and each of these can be run via a separate <span class="sb" style="color: #d14;">`augur`</span> command.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">If you look at the <span class="p">[</span><span class="nv" style="color: #008080;">other tutorials</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.nextstrain.org/en/latest/tutorials/index.html</span><span class="p">)</span>, each one uses a slightly different combination of <span class="sb" style="color: #d14;">`augur`</span> commands depending on the pathogen.</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Snakemake</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">While it is possible to run a build by running each of the individual steps, we typically group these together into a make-type file.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Snakemake</span><span class="p">](</span><span class="sx" style="color: #d14;">https://snakemake.readthedocs.io/en/stable/index.html</span><span class="p">)</span> is "a tool to create reproducible and scalable data analyses... via a human-readable, Python-based language."</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Snakemake is installed as part of the [conda environment](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html#install-augur-auspice-with-conda) or the [docker container](https://docs.nextstrain.org/en/latest/guides/install/cli-install.html).</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">If you ever see a build which has a "Snakefile" then you can run this by typing <span class="sb" style="color: #d14;">`snakemake --cores 1`</span> or <span class="sb" style="color: #d14;">`nextstrain build --cpus 1 .`</span>, respectively.</span></pre>

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<br>

</li>

<li id="d0153cac95479af9bfb99b746b633bc8255bb53a">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#d0153cac95479af9bfb99b746b633bc8255bb53a"><strong>docs/index.rst</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">@@ -5,9 +5,19 @@ Augur: A bioinformatics toolkit for phylogenetic analysis</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">    *One held to foretell events by omens.*</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">    (`Merriam-Webster <https://www.merriam-webster.com/dictionary/augur>`__)</span>

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.. note::</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">   The documentation you are viewing is Augur's reference guide, which means it is information-oriented and targeted at users who just need info about how Augur works.</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">    </span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">   * If you have a question about how to achieve a specific goal with Augur, check out our :doc:`Augur-focused How-to Guides section <docs.nextstrain.org:guides/bioinformatics/index>` in the main Nextstrain documentation.</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">   * If you want to learn the basics of how to use Augur from scratch, check out our :doc:`Zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>` in the main Nextstrain documentation.</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">   * If you want to understand how Augur fits together with Auspice to visualize results, check out our :doc:`Data Formats section <docs.nextstrain.org:reference/formats/data-formats>` in the main Nextstrain documentation.</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Augur is a bioinformatics toolkit to track evolution from sequence and serological data.</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">It provides a collection of commands which are designed to be composable into larger processing pipelines.</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Augur originated as part of `Nextstrain <https://nextstrain.org>`__, an open-source project to harness the scientific and public health potential of pathogen genome data.</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">All source code is available on `GitHub <https://github.com/nextstrain/augur>`__.</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">.. note:: We have just released version 6 of augur -- `check our upgrading guide <releases/migrating-v5-v6.html>`__</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></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">@@ -26,7 +36,6 @@ The ``refine`` step is necessary to ensure that cross-referencing between tree n</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">The different augur modules can be strung together by workflow managers like snakemake and nextflow.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">The nextstrain team uses `snakemake <https://snakemake.readthedocs.io/en/stable/>`__ to run and manage the different analysis that you see on `nextstrain.org <https://nextstrain.org>`__.</span>

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

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">.. toctree::</span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">   :maxdepth: 2</span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">   :caption: Table of contents</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="46" 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">@@ -37,7 +46,6 @@ The nextstrain team uses `snakemake <https://snakemake.readthedocs.io/en/stable/</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">   usage/usage</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">   releases/releases</span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">   faq/faq</span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">   tutorials/tutorials</span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">   examples/examples</span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">   api/api</span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">   authors/authors</span></pre>

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<br>

</li>

<li id="e8b985c0ef42231b85fdf9aa97fbad5fff94be7f">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#e8b985c0ef42231b85fdf9aa97fbad5fff94be7f"><strong>docs/releases/migrating-v5-v6.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="119" 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">@@ -119,7 +119,8 @@ These may have been inferred for internal nodes by Augur functions like `augur t</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown">Certain traits have a geographic interpretation, e.g. "country".</span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown">Auspice will attempt to display these traits on a map (and provide a drop-down to switch between them if there are more than one).</span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="gt" style="color: #a00;"></span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"><span class="gt" style="color: #a00;">> _Make sure that these have corresponding entry in the lat-longs TSV file supplied to `export`. See how to do this [here](/faq/lat_longs)._</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="gt" style="color: #a00;">> _Make sure that these have corresponding entry in the lat-longs TSV file supplied to `export`. See how to do this [here](https://docs.nextstrain.org/en/latest/guides/bioinformatics/lat_longs.html)._</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="p"></span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"><span class="p"></span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="p"></span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="p">---</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" 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="529" 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">@@ -528,5 +529,6 @@ In Auspice v2, all values are now displayed exactly as they arrive, allowing use</td>

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="markdown"><span class="sb" style="color: #d14;"></span></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="markdown"><span class="sb" style="color: #d14;">Don't forget to also change them in any custom lat-long and/or coloring files you are using. We've also become stricter about the format of the files that pass in color and lat-long information. Previously, it didn't matter if columns were separated by spaces or tabs - now, they must be separated by tabs.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="531" 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="LC531" class="line" lang="markdown"><span class="sb" style="color: #d14;"></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="markdown"><span class="sb" style="color: #d14;">You can find out more about how to add [custom coloring](/faq/colors) and [lat-long](/faq/lat_longs) values.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="markdown"><span class="sb" style="color: #d14;">You can find out more about how to add [custom coloring](https://docs.nextstrain.org/en/latest/guides/bioinformatics/colors.html) and [lat-long](https://docs.nextstrain.org/en/latest/guides/bioinformatics/lat_longs.html) values.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="markdown"><span class="sb" style="color: #d14;"></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="markdown"><span class="sb" style="color: #d14;">If you use the command `</span>parse<span class="sb" style="color: #d14;">` to generate a metadata table from fields in a fasta header, you can use the flag `</span>--prettify-fields<span class="sb" style="color: #d14;">` to apply some prettifying operations to specific metadata entries, see the documentation [`</span>parse<span class="err" style="color: #a61717; background-color: #e3d2d2;">`</span>](/usage/cli/parse).</span></pre>

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</li>

<li id="1f374f74b0b9c0ebde03840d6c75d5e2e9f516de">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#1f374f74b0b9c0ebde03840d6c75d5e2e9f516de"><strong>docs/releases/v6.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="46" 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">@@ -46,7 +46,7 @@ Users can ask for this output and specify a file name using `--output-sequences`</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">style=</span><span class="s" style="color: #d14;">'color: orange'</span><span class="nt" style="color: #000080;">></span>Deprecation warning:<span class="nt" style="color: #000080;"></span></span> The argument <span class="sb" style="color: #d14;">`--output`</span> is now deprecated. Please use <span class="sb" style="color: #d14;">`--output-node-data`</span> instead.</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>

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<td class="diff-line-num new_line" data-linenumber="48" 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="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Import BEAST MCC trees</span></span>

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<td class="diff-line-num old old_line" data-linenumber="49" 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="LC49" class="line" lang="markdown">We now have instructions and functionality to import BEAST trees, see <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 right">/faq/import-beast</span></span><span class="p">)</span>.</span>

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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="markdown">We now have instructions and functionality to import BEAST trees, see <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 right">https://docs.nextstrain.org/en/latest/guides/bioinformatics/import-beast.html</span></span><span class="p">)</span>.</span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Prettifying of strings</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" 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="LC52" class="line" lang="markdown">Previous auspice version "prettified" metadata strings (like changing 'north_america' to 'North America').</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="110" 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">@@ -110,4 +110,4 @@ We've tried to use redirects to ensure that all the old links continue to work.</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="p">*</span> Errors in formatting of input files (e.g. metadata files, Auspice config files) weren't handled nicely, often resulting in hard-to-interpret stack traces.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown">We now try to catch these and print an error indicating the offending file.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown"><span class="p">*</span> Tests using Python version 2 have now been removed.</span></pre>

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<td class="old_line diff-line-num" 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">\ No newline at end of file</td>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="LC113" class="line" lang="markdown"><span class="p">*</span> Tests using Python version 2 have now been removed.</span></pre>

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<br>

</li>

<li id="6ceb651c15e9f3ce63e7396537e81e5b1377b418">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#6ceb651c15e9f3ce63e7396537e81e5b1377b418"><strong>docs/tutorials/tb_tutorial.md</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,7 +7,7 @@ As in the Zika fasta-input [tutorial](zika_tutorial), we'll build up a Snakefile</td>

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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;">## Setup</span></span>

</pre>

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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">To run this tutorial you'll need to <span class="p">[</span><span class="nv" style="color: #008080;">install augur</span><span class="p">](</span><span class="sx" style="color: #d14;">../<span class="idiff left right">installation/installation</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">install Snakemake</span><span class="p">](</span><span class="sx" style="color: #d14;">https://snakemake.readthedocs.io/en/stable/getting_started/installation.html</span><span class="p">)</span>.</span>

</pre>

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</td>

<td class="diff-line-num new new_line" 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">To run this tutorial you'll need to <span class="p">[</span><span class="nv" style="color: #008080;">install augur</span><span class="p">](</span><span class="sx" style="color: #d14;">../<span class="idiff left right">guides/install/augur_install.md</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">install Snakemake</span><span class="p">](</span><span class="sx" style="color: #d14;">https://snakemake.readthedocs.io/en/stable/getting_started/installation.html</span><span class="p">)</span>.</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;">## Build steps</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">Nextstrain builds typically require the following steps:</span>

</pre>

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<br>

</li>

<li id="c82653f427e53da3edca7577d17b03fa3a909b8b">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#c82653f427e53da3edca7577d17b03fa3a909b8b"><strong>docs/tutorials/tutorials.rst</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">=========</span>

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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

</td>

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

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.. note:: We have just released version 6 of augur -- `check our upgrading guide <../releases/migrating-v5-v6.html>`__</span>

</pre>

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6

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.. toctree::</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">   :maxdepth: 1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">   :caption: Available tutorials</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

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</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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11

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">   zika_tutorial</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">   tb_tutorial</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="117e91c7f77ddab94ba103f3fddbb7e10ec356e7">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#117e91c7f77ddab94ba103f3fddbb7e10ec356e7"><strong>docs/tutorials/zika_tutorial.md</strong></a>

<hr>

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

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,7 +7,7 @@ We will work off the tutorial for Zika virus on the [nextstrain web site](https:</td>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="7" 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">

7

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

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

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line" data-linenumber="8" 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">

8

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line" data-linenumber="9" 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">

9

</td>

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

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

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">To run this tutorial you'll need to <span class="p">[</span><span class="nv" style="color: #008080;">install augur</span><span class="p">](</span><span class="sx" style="color: #d14;">../<span class="idiff left right">installation/installation</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">install Snakemake</span><span class="p">](</span><span class="sx" style="color: #d14;">https://snakemake.readthedocs.io/en/stable/getting_started/installation.html</span><span class="p">)</span>.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

10

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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="LC10" class="line" lang="markdown">To run this tutorial you'll need to <span class="p">[</span><span class="nv" style="color: #008080;">install augur</span><span class="p">](</span><span class="sx" style="color: #d14;">../<span class="idiff left right">guides/install/augur_install.md</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">install Snakemake</span><span class="p">](</span><span class="sx" style="color: #d14;">https://snakemake.readthedocs.io/en/stable/getting_started/installation.html</span><span class="p">)</span>.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

</td>

<td class="diff-line-num new_line" data-linenumber="11" 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">

11

</td>

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

</td>

<td class="diff-line-num new_line" data-linenumber="12" 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">

12

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

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

</td>

<td class="diff-line-num new_line" data-linenumber="13" 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">

13

</td>

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d6d5362abd39a9db0355122f2f394a267d81513f">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#d6d5362abd39a9db0355122f2f394a267d81513f"><strong>docs/usage/cli/filter.rst</strong></a>

<hr>

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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">@@ -15,7 +15,7 @@ augur filter</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">How we subsample sequences in the zika-tutoral</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">==============================================</span>

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

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">As an example, we'll look that the ``filter`` command in greater detail using material form the <span class="idiff left right">`zika tutorial <../../tutorials/zika_tutorial.html>`__</span>.</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">As an example, we'll look that the ``filter`` command in greater detail using material form the <span class="idiff left right">:doc:`zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>`</span>.</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">The filter command allows you to selected various subsets of your input data for different types of analysis.</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">A simple example use of this command would be</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></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">@@ -45,7 +45,7 @@ To drop such strains, you can pass the name of this file to the augur filter com</td>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">             --output filtered.fasta</span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">(To improve legibility, we have wrapped the command across multiple lines.)</span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the <span class="idiff left right">`zika tutorial <zika_tutorial.html>`__</span>, you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strains.txt`` file.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the <span class="idiff left right">:doc:`zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>`</span>, you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strains.txt`` file.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Another common filtering operation is subsetting of data to a achieve a more even spatio-temporal distribution or to cut-down data set size to more manageable numbers.</span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">The filter command allows you to select a specific number of sequences from specific groups, for example one sequence per month from each country:</span>

</pre>

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<br>

</li>

<li id="51dfac45ef9ee65b645bb4efa64dc86e4d8c2c3b">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#51dfac45ef9ee65b645bb4efa64dc86e4d8c2c3b"><strong>docs/usage/usage.rst</strong></a>

<hr>

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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">@@ -26,6 +26,5 @@ For instance, the documentation for `augur filter <./cli/filter.html>`__ shows h</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">   :maxdepth: 2</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">   cli/cli</span>

</pre>

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29

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">   augur_snakemake</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">   envvars</span></pre>

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</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="49" 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">@@ -49,11 +49,11 @@ setuptools.setup(</td>

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<td class="diff-line-num old_line" data-linenumber="49" 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">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">    <span class="n" style="color: #333;">python_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'>={}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">min_version</span><span class="p">)),</span></span>

</pre>

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50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">    <span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" 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="LC51" class="line" lang="python">        <span class="s" style="color: #d14;">"bcbio-gff >=0.6.0, ==0.6.*"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python">        <span class="s" style="color: #d14;">"biopython >=1.67, <=1.7<span class="idiff left right">8</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="52" 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="LC52" class="line" lang="python">        <span class="s" style="color: #d14;">"biopython >=1.67, <=1.7<span class="idiff left right">6</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" 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="diff-line-num new_line" data-linenumber="53" 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="LC53" class="line" lang="python">        <span class="s" style="color: #d14;">"jsonschema >=3.0.0, ==3.*"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" 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="diff-line-num new_line" data-linenumber="54" 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="LC54" class="line" lang="python">        <span class="s" style="color: #d14;">"packaging >=19.2"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" 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">

55

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<td class="diff-line-num new_line" data-linenumber="55" 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="LC55" class="line" lang="python">        <span class="s" style="color: #d14;">"pandas >=1.0.0, ==1.*"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" 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="diff-line-num new_line old" data-linenumber="56" 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="LC56" class="line" lang="python">        <span class="s" style="color: #d14;">"phylo-treetime <span class="idiff left right">>=0.7.4, ==0.7</span>.*"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" 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="LC56" class="line" lang="python">        <span class="s" style="color: #d14;">"phylo-treetime <span class="idiff left right">==0.8</span>.*"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="57" 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="LC57" class="line" lang="python">    <span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" 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">

58

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<td class="diff-line-num new_line" data-linenumber="58" 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="LC58" class="line" lang="python">    <span class="n" style="color: #333;">extras_require</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" 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="diff-line-num new_line" data-linenumber="59" 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="LC59" class="line" lang="python">        <span class="s" style="color: #d14;">'full'</span><span class="p">:</span> <span class="p">[</span></span>

</pre>

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</table>

<br>

</li>

<li id="6788c84297b185802f92db51db36c33eb731ecfe">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#6788c84297b185802f92db51db36c33eb731ecfe"><strong>tests/builds/zika.t</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" 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">@@ -75,8 +75,6 @@ Build a time tree from the existing tree topology, the multiple sequence alignme</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --date-inference marginal \</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" 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="LC76" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --clock-filter-iqd 4 \</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" 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="LC77" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --seed 314159 > /dev/null</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="perl"><span class="s1" style="color: #d14;">  */treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify </span><span class="p">'</span><span class="nv" style="color: #008080;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">object</span><span class="p">'</span><span class="s1" style="color: #d14;"> when creating the ndarray (glob)</span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="perl"><span class="s1" style="color: #d14;">    [0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" 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="LC79" class="line" lang="perl"><span class="s1" style="color: #d14;">Confirm that TreeTime trees match expected topology and branch lengths.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" 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="LC80" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,8 +105,6 @@ Infer ancestral sequences from the tree.</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --infer-ambiguous \</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --output-node-data "$TMP/out/nt_muts.json" \</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"><span class="s1" style="color: #d14;">  >  --inference joint > /dev/null</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="perl"><span class="s1" style="color: #d14;">  */treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify </span><span class="p">'</span><span class="nv" style="color: #008080;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">object</span><span class="p">'</span><span class="s1" style="color: #d14;"> when creating the ndarray (glob)</span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="perl"><span class="s1" style="color: #d14;">    [0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" 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="diff-line-num new_line" data-linenumber="109" 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="LC109" class="line" lang="perl"><span class="s1" style="color: #d14;">  $ diff -u --ignore-matching-lines version "results/nt_muts.json" "$TMP/out/nt_muts.json"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" 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="LC110" class="line" lang="perl"></span>

</pre>

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<br>

</li>

<li id="d765401a067b8ae8f8d883fc416c80ca1d23904f">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#d765401a067b8ae8f8d883fc416c80ca1d23904f"><strong>tests/functional/ancestral.t</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,8 +11,6 @@ The default is to infer ambiguous bases, so there should not be N bases in the i</td>

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<pre style="margin: 0;"> <span id="LC11" 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;">alignment</span> <span class="nv" style="color: #008080;">ancestral</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">aligned</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span> <span class="o" style="font-weight: 600;">\</span></span>

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<pre style="margin: 0;"> <span id="LC12" 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;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_mutations.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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="diff-line-num new_line" data-linenumber="13" 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="LC13" 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;">sequences</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</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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<td class="diff-line-num old old_line" data-linenumber="14" 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="diff-line-num new_line old" data-linenumber="14" 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="LC14" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="15" 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="diff-line-num new_line old" data-linenumber="14" 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="LC15" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl">  <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">grep</span> <span class="nv" style="color: #008080;">N</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</span><span class="p">"</span></span>

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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="perl">  <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">NODE_0000000</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,8 +24,6 @@ There should not be N bases in the inferred output sequences.</td>

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<td class="diff-line-num old_line" data-linenumber="26" 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="LC24" 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;">infer</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">ambiguous</span> <span class="o" style="font-weight: 600;">\</span></span>

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<pre style="margin: 0;"> <span id="LC25" 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;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_mutations.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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="diff-line-num new_line" data-linenumber="26" 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="LC26" 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;">sequences</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</span><span class="p">"</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="27" 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="LC30" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl">  <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">grep</span> <span class="nv" style="color: #008080;">N</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</span><span class="p">"</span></span>

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<td class="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="perl">  <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">NODE_0000000</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" 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">@@ -41,8 +37,6 @@ There be N bases in the inferred output sequences.</td>

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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;">keep</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">ambiguous</span> <span class="o" style="font-weight: 600;">\</span></span>

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<pre style="margin: 0;"> <span id="LC38" 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;">node</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">data</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_mutations.json</span><span class="p">"</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC39" 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;">sequences</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</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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<pre style="margin: 0;">-<span id="LC44" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl">  <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">grep</span> <span class="nv" style="color: #008080;">N</span> <span class="p">"</span><span class="si" style="color: #d14;">$TMP</span><span class="s2" style="color: #d14;">/ancestral_sequences.fasta</span><span class="p">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" 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="LC42" class="line" lang="perl">  <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">NODE_0000000</span></span>

</pre>

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<br>

</li>

<li id="9753651334e00be71d51aba2fccf83cd1d0508c5">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#9753651334e00be71d51aba2fccf83cd1d0508c5"><strong>tests/functional/refine.t</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,8 +17,6 @@ Try building a time tree.</td>

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<td class="diff-line-num old_line" 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="perl">  <span class="o" style="font-weight: 600;">></span>  <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">date</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">inference</span> <span class="nv" style="color: #008080;">marginal</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num old_line" 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">

18

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<td class="diff-line-num new_line" 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">

18

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<pre style="margin: 0;"> <span id="LC18" 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;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;"> <span id="LC19" 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;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC20" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

</pre>

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21

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC21" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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<td class="diff-line-num 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">

20

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">TreeTime</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="o" style="font-weight: 600;">.</span></span>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" 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">@@ -40,8 +38,6 @@ Build a time tree with mutations as the reported divergence unit.</td>

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<pre style="margin: 0;"> <span id="LC38" 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;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC39" 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;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC40" 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;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC43" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC44" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="42" 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="LC42" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">TreeTime</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="o" style="font-weight: 600;">.</span></span>

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<td class="diff-line-num new_line" data-linenumber="43" 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="LC43" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" 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="58" 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">@@ -62,8 +58,6 @@ This is one way to get named internal nodes for downstream analyses and does not</td>

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<pre style="margin: 0;"> <span id="LC58" 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;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>

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<pre style="margin: 0;"> <span id="LC59" 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;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>

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<pre style="margin: 0;"> <span id="LC60" 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;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</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;">site</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="66" 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">

66

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<td class="diff-line-num new_line old" data-linenumber="61" 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="LC66" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

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67

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<td class="diff-line-num new_line" data-linenumber="61" 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">

61

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="68" 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">

68

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<td class="diff-line-num new_line" data-linenumber="62" 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="LC62" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="p">,</span> <span class="nv" style="color: #008080;">given</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">should</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">be</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>

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<td class="diff-line-num old_line" data-linenumber="69" 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="diff-line-num new_line" data-linenumber="63" 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="LC63" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="81" 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">@@ -87,8 +81,6 @@ This approach only works when we provide an alignment FASTA.</td>

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<td class="diff-line-num old_line" data-linenumber="87" 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="diff-line-num new_line" data-linenumber="81" 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="LC81" 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;">clock</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">iqd</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num old_line" data-linenumber="88" 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="diff-line-num new_line" data-linenumber="82" 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="LC82" 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;">seed</span> <span class="mi" style="color: #099;">314159</span> <span class="o" style="font-weight: 600;">\</span></span>

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<td class="diff-line-num new_line" data-linenumber="83" 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="LC83" 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;">divergence</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">units</span> <span class="nv" style="color: #008080;">mutations</span> <span class="o" style="font-weight: 600;">></span> <span class="sr" style="color: #009926;">/dev/null</span></span>

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<td class="diff-line-num new_line old" data-linenumber="84" 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="LC90" class="line" lang="perl">  <span class="o" style="font-weight: 600;">*</span><span class="sr" style="color: #009926;">/treetime/aa</span><span class="nv" style="color: #008080;">_models</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">py:108:</span> <span class="nv" style="color: #008080;">VisibleDeprecationWarning:</span> <span class="nv" style="color: #008080;">Creating</span> <span class="nv" style="color: #008080;">an</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="nv" style="color: #008080;">from</span> <span class="nv" style="color: #008080;">ragged</span> <span class="nv" style="color: #008080;">nested</span> <span class="nv" style="color: #008080;">sequences</span> <span class="p">(</span><span class="nv" style="color: #008080;">which</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">a</span> <span class="nv" style="color: #008080;">list</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuple</span> <span class="nv" style="color: #008080;">of</span> <span class="nv" style="color: #008080;">lists</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">tuples</span><span class="o" style="font-weight: 600;">-</span><span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">ndarrays</span> <span class="nv" style="color: #008080;">with</span> <span class="nv" style="color: #008080;">different</span> <span class="nv" style="color: #008080;">lengths</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">shapes</span><span class="p">)</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">deprecated</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">If</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">meant</span> <span class="nv" style="color: #008080;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="nv" style="color: #008080;">this</span><span class="p">,</span> <span class="nv" style="color: #008080;">you</span> <span class="nv" style="color: #008080;">must</span> <span class="nv" style="color: #008080;">specify</span> <span class="p">'</span><span class="s1" style="color: #d14;">dtype=object</span><span class="p">'</span> <span class="nv" style="color: #008080;">when</span> <span class="nv" style="color: #008080;">creating</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">ndarray</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="perl">    <span class="p">[</span><span class="mf" style="color: #099;">0.800038509951648</span><span class="p">,</span> <span class="mf" style="color: #099;">1.20274751778601</span><span class="p">,</span> <span class="mf" style="color: #099;">1.55207513886163</span><span class="p">,</span> <span class="mf" style="color: #099;">1.46600946033173</span><span class="p">,</span> <span class="mf" style="color: #099;">0.830022143283238</span><span class="p">,</span> <span class="mf" style="color: #099;">1.5416250309563</span><span class="p">,</span> <span class="mf" style="color: #099;">1.53255698189437</span><span class="p">,</span> <span class="mf" style="color: #099;">1.41208067821187</span><span class="p">,</span> <span class="mf" style="color: #099;">1.47469999960758</span><span class="p">,</span> <span class="mf" style="color: #099;">0.351200119909572</span><span class="p">,</span> <span class="mf" style="color: #099;">0.570542199221932</span><span class="p">,</span> <span class="mf" style="color: #099;">1.21378822764856</span><span class="p">,</span> <span class="mf" style="color: #099;">0.609532859331199</span><span class="p">,</span> <span class="mf" style="color: #099;">0.692733248746636</span><span class="p">,</span> <span class="mf" style="color: #099;">1.40887880416009</span><span class="p">,</span> <span class="mf" style="color: #099;">1.02015839286433</span><span class="p">,</span> <span class="mf" style="color: #099;">0.807404666228614</span><span class="p">,</span> <span class="mf" style="color: #099;">1.268589159299</span><span class="p">,</span> <span class="mf" style="color: #099;">0.933095433689795</span><span class="p">]</span></span>

</pre>

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92

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<td class="diff-line-num new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<td class="diff-line-num new_line" data-linenumber="85" 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">

85

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"><span class="nv" style="color: #008080;">Confirm</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">trees</span> <span class="nv" style="color: #008080;">match</span> <span class="nv" style="color: #008080;">expected</span> <span class="nv" style="color: #008080;">topology</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">branch</span> <span class="nv" style="color: #008080;">lengths</span><span class="p">,</span> <span class="nv" style="color: #008080;">given</span> <span class="nv" style="color: #008080;">that</span> <span class="nv" style="color: #008080;">the</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">should</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">be</span> <span class="nv" style="color: #008080;">a</span> <span class="nb" style="color: #0086b3;">time</span> <span class="nv" style="color: #008080;">tree</span><span class="o" style="font-weight: 600;">.</span></span>

</pre>

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94

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<td class="diff-line-num new_line" data-linenumber="86" 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="LC86" class="line" lang="perl"></span>

</pre>

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<br>

</li>

<li id="dc10ba1af84013a385b35192d66ceb8036cefb1d">

<a href="https://salsa.debian.org/med-team/augur/-/commit/4b456b7906192b5c0a9dc2f0de027e3a021f82f4#dc10ba1af84013a385b35192d66ceb8036cefb1d"><strong>tests/test_utils.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" 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="91" 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">@@ -91,7 +91,7 @@ class TestUtils:</td>

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<td class="diff-line-num new_line" data-linenumber="91" 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="LC91" class="line" lang="python">            <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">write</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 class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">bed_lines</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">            <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">read_bed_file</span><span class="p">(</span><span class="n" style="color: #333;">bed_file</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="95" 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="LC95" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_mask_file_drm_file</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" 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="LC96" class="line" lang="python">        <span class="s" style="color: #d14;">"""read_mask_file should handle drm files as well"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">        <span class="n" style="color: #333;">drm_file</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;">"temp.drm"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" 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="100" 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">@@ -100,3 +100,32 @@ class TestUtils:</td>

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<td class="diff-line-num new_line" data-linenumber="100" 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="LC100" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">drm_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" 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="LC101" class="line" lang="python">            <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">write</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 class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">drm_lines</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">read_mask_file</span><span class="p">(</span><span class="n" style="color: #333;">drm_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_sites</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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="LC103" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_is_date_ambiguous</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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="LC105" class="line" lang="python">        <span class="s" style="color: #d14;">"""is_date_ambiguous should return true for ambiguous dates and false for valid dates."""</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Test complete date strings with ambiguous values.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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="LC107" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-0X-0X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"any"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX-09"</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="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-03-XX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"201X-03-09"</span><span class="p">,</span> <span class="s" style="color: #d14;">"year"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"20XX-01-09"</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="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" 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="LC112" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX-03"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"20XX-01-03"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Test incomplete date strings with ambiguous values.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" 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="LC116" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019"</span><span class="p">,</span> <span class="s" style="color: #d14;">"any"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"201X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"year"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" 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="LC118" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX"</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="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="119" 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="LC119" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-10"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"any"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" 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">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="122" 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">

122

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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="LC122" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="123" 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">

123

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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="LC123" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Test complete date strings without ambiguous dates for the requested field.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="124" 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">

124

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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="LC124" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-09-03"</span><span class="p">,</span> <span class="s" style="color: #d14;">"any"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="125" 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">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-03-XX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"month"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="126" 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">

126

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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="LC126" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-09-03"</span><span class="p">,</span> <span class="s" style="color: #d14;">"day"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="127" 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">

127

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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="LC127" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-XX-XX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"year"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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">

128

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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="LC128" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="129" 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">

129

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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="LC129" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Test incomplete date strings without ambiguous dates for the requested fields.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="130" 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">

130

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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="LC130" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019"</span><span class="p">,</span> <span class="s" style="color: #d14;">"year"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="131" 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">

131

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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="LC131" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">is_date_ambiguous</span><span class="p">(</span><span class="s" style="color: #d14;">"2019-10"</span><span class="p">,</span> <span class="s" style="color: #d14;">"month"</span><span class="p">)</span></span></pre>

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